Before Getting Started You Should Know...
Even though a 2 stroke engine is incredibly simple with very few moving parts and they're relatively inexpensive to service and maintain, there are still several points that need to be addressed during the tear down / disassembly and reassembly of the engine so as to avoid ruined parts and wasted money, so in an effort to help those that may not be experienced in performing this type of service, this whole process is broken down into several different categories, all of which can be reached through the links provided below which categorize these processes.
Before getting too far ahead of the rest of us, it's important to note that If there's ever been a case for needing a factory service manual specific to the motorcycle being serviced, This Is It, although if you can't wait for a service manual to arrive, the tips below will do a pretty good job of guiding you through rebuilding the top end of a 2 stroke dirt bike.
Just keep in mind that the reason a service manual applicable to the motorcycle being serviced is necessary and indispensable, is due to the variances in torque and clearance, or wear limit specifications between brands and displacements of individual motorcycles, as well as the differences in the way that power valves are assembled, adjusted and timed, all of which is provided in detail within a service manual specific to each motorcycle.
Now with all that behind us, Let's Get Right Into It
How Often Should I Tear it Down and Replace the Top End?
This varies as we'll discuss below, but people often put off pulling the top end apart as it looks like quite the job, and they often feel that if it runs, it's good enough for another outing or race. What people often don't realize is that if they were to do a freshening up of the top end Before it quits running, they greatly reduce the chances of broken engine cases, or other engine damage, while also enjoying a crispier throttle response, and a better performing motorcycle overall, while also reducing the spooge that is drooling out of everywhere from the cylinder to the tip of the silencer.
It's important to realize that time between rebuilds can vary greatly depending on the bike's use and maintenance being performed, which includes the frequency of air filter services and the condition of the intake tract, but there are still even more factors than this to consider which we'll cover in detail below.
If you're wondering when the manufacturer of your specific bike recommends the top end be replaced, a factory service manual specific to the motorcycle will provide specific intervals, but even these recommendations should still only be interpreted as rough guidelines, as maintenance (or lack of) among other factors can have a huge influence on how often the motor should be torn down.
If you're without a service manual, there's a table below which specifies tear down intervals of when a 2 stroke's top end should be overhauled, but again, these values should only be considered a rough guideline, as in addition to time on the engine, there are other factors which are discussed below that need to be considered when determining when to tear down the top end of a 2 stroke engine.
Bottom line is that after consideration of the points discussed below, you should be able to establish a pretty good idea of when to tear it down without resorting to any charts or tables, although if a compression test is performed and the engine is low on compression, there should be no doubt as to the need for disassembly.
What To Consider When Determining How Often To Rebuild A 2 Stroke
- How Long It's Been Since the Last Rebuild
- There are widely accepted suggested intervals for when to tear down a 2 stroke, but these intervals are based off of ideal conditions where routine maintenance is regularly performed and the motorcycle is maintained at it's highest level. If you don't know the last time the top end was apart, (If Ever) or if you recently bought a used dirt bike and aren't sure if or when the previous owner last did a top end, it would be a good idea to perform a top end rebuild as this will enable you to accurately evaluate the top end's condition, then you can consider an overhaul at these suggested intervals.
- Type of Use (Recreational vs Race Use)
- The use that the motorcycle sees can have a strong influence on the frequency of top end rebuilds, as bikes that are raced are often freshened up (Piston Rings or Piston and Rings Replaced) at set intervals so as to maintain optimum performance. On the other end of the spectrum are the dirt bikes which are only ridden recreationally and these often suffer from a lack of proper maintenance so with this in mind, a compression test can give you a rough indication of the top end's condition and can be instrumental in determining when to rebuild the top end.
- Condition of the Air Filter or Frequency of Air Filter Maintenance
- Neglecting the air filter maintenance on dirt bikes is one of the best ways of wearing out a top end, (not to mention what it does to crank and rod bearings) as running a dirty air filter can starve the engine for air, as well as neglected air filters often allow unfiltered air to pass through unbeknownst rips or separations of the filter element allowing unfiltered air to be ingested ultimately resulting in piston and cylinder damage, as well as accelerated wear of the connecting rod and crankshaft main bearings. Anytime you're servicing the air filter, If dirt particles are present in the intake tract, you may want to consider tearing it down so you can take a look at the cylinder walls for any evidence of scoring or other damage.
- Condition of the Intake Tract
- In addition to properly maintaining the air filter, it's critical that the intake is properly sealed as any loose clamps or improperly sealed air boots will allow unfiltered air to be introduced to the air entering the engine. Just keep in mind that if there's ever been any air leaks such as from a damaged or improperly installed intake boot, or there's history or evidence of an air filter that wasn't properly installed, or had rips and there's dirt visible in the intake, a tear down should be in order so as to be able to inspect the cylinder and piston for any resultant damage caused from unfiltered air reaching the motor.
- Performance of the Engine
- The performance of the engine can be an indicator of whether or not a top end needs disassembled, as a 2 stroke engine which normally runs good but now runs flat with no other problems (such as carburetion issues) can be indicative of a stuck power valve. Fortunately, some manufacturers have a method of checking the powervalve's operation without much disassembly of the motorcycle and this is generally well detailed in a factory service manual specific to the motorcycle.
Note: Although some power valves can be disassembled with the cylinder on the bike, it's best to remove the cylinder any time a power valve cleaning is performed as doing so will enable you to perform a better cleaning of the power valve and associated passages, as well as removing the cylinder will allow you to inspect the cylinder or re-ring the piston if necessary.
- Evidence of Any Leaks
- Any time an engine shows any evidence of crankcase, cylinder or cylinder head leaks, the top end or complete engine should be disassembled to correct the matter, as crankcase leaks, (including a leaking LH crank seal), or leaks around the base of the cylinder can cause an excessively lean condition which can result in engine damage. Alternatively, if it's noticed that coolant is leaking from the cylinder head or cylinder base it's important that this is corrected as coolant leaks which allow coolant into the cylinder can cause cylinder, cylinder head and / or piston damage.
Note: Removal of the exhaust pipe will allow you to inspect the piston for signs of "blow-by" (a slang term for combustion gasses leaking past the piston rings). If it's determined that the engine is suffering a power loss, and there's evidence of blow-by on the piston as evidenced by looking in through the exhaust port, it's recommended that the top end be disassembled as this is an indication that the piston rings are not sealing to the cylinder wall properly.
- Type or Ratio of Premix and / or Grade of Fuel Being Used
- The type and ratio of premix being used can influence or prolong the wear of the top end, although what's common is bikes that have been run on too low of octane fuel for the compression of the motor, or running an excessively rich or lean oil / fuel mixture which ultimately results in piston damage, all of which will require disassembly of the top end to correct.
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|Tear Down Intervals
Track the Run Time with an Hour Meter and You'll Forever Know When to Change the Oil and Perform Other Maintenance Without Any Guessing.
How To Tear It Down
If you're not sure where to begin on tearing down the top end of a 2 stroke, don't sweat it as freshening up the top end on a 2 stroke dirt bike with new ring(s) or a new piston and ring(s) is not difficult, but it is recommended that you pick up a factory service manual specific to the motorcycle beforehand, as these are full of torque, measurement and wear specs that this article could't possibly cover, yet you'll be needing to refer to.
If you're without a service manual, the whole process is broken down into 10 simple steps that'll have you replacing the piston and ring(s) on any 2 stroke dirt bike in no time, but just remember, if you don't have wear specs then you have to assume that anything that looks worn, probably Is.
Before beginning disassembly of anything, it's important that you're working with a clean motorcycle. Even though you may feel you've got washing a dirt bike in the bag, you may want to review this article on washing a dirt bike, as doing so will ensure there won't be any dirt getting into places it shouldn't be upon disassembly.
Now, with a clean motorcycle, let's begin...
- Drain the Coolant
On liquid cooled motorcycles, you're going to need to drain the coolant and it's advisable to do so before placing the motorcycle on a Work Stand for service as doing things this way will allow you to catch nearly all of the coolant vs having it run all over the stand and the floor.
- Remove the Seat and Subframe
Removing the seat and subframe is not always necessary, nor is it possible to remove the subframe on some bikes, although the majority of off-road motorcycles do have removable sub-frames and removing this complete with the airbox will make getting the carburetor in and out much easier.
- Remove the Gas Tank and Radiator Shrouds
Removing the fuel tank with the radiator shrouds attached will allow you direct access to the top of the engine, but once the fuel line is disconnected from the carburetor, be sure to cap both the fuel line and the carburetor inlet so as to prevent any contaminants from entering the fuel system.
- Now the Radiator(s)
A top end can often be rebuilt without removal of the radiator(s) but I can assure you that removing one or both radiators will allow you much more room for lifting the cylinder off, or replacing the cylinder upon reassembly without damaging the piston or rings as well as doing so will allow you to inspect the wiring that is often routed in this area.
- Remove the Top Motor Mount
Now remove the upper engine mount while paying close attention to any washers, shims or spacers between the motor mount plates and the frame or the cylinder head as these will need to be reinstalled so as to relieve any potential stress or binding of the motor in the mounts.
- Remove the Spark Plug Wire, Spark Plug, Hoses and Carburetor
Removal of the spark plug wire, the spark plug, the coolant hose(s) and the carburetor is pretty straightforward but be sure to handle the carburetor carefully then wrap it in a clean rag and drape it (with the cable attached) over the handlebars and out of the way.
- Remove the Exhaust
Removing the exhaust is accomplished by removing the springs which secure it to the cylinder, as well as removal of a lower and rear mounting bolt but this should be fairly straightforward.
- Disconnect any Power Valve Linkage
On motorcycles with an external powervalve link, it's important that this is disconnected prior to lifting the cylinder off of the cases, otherwise the cylinder will not be able to be removed.
Note: Some models do not require any linkage to be disconnected before removal of the cylinder although if there is any cover that joins the cylinder and engine cover, chances are there is a link within but again, there is where a factory service manual proves indispensable.
When loosening the Cylinder Head and Cylinder Base Nuts,
Make Sure You Do So in a Criss Cross Pattern In Steps
- Remove the Cylinder Head Nuts and Cylinder Head
It's important that during removal of the cylinder head nuts that a box end wrench or a socket (likely a 12mm) is used so as to not round the corners off, as well as these and the cylinder base nuts should be loosened in steps and in a criss-cross pattern so as to prevent distortion of the cylinder head or cylinder deck.
- Remove the Cylinder Base Nuts, Then the Cylinder
Finally, using a box end wrench (likely a 14mm), remove the 4 nuts securing the cylinder to the engine cases and once free, carefully lift the cylinder straight up off of the dowels, studs and piston while supporting the piston and rod with your other hand.
Note: On some bikes, there may be a 4th nut concealed within a cover attached to the side of the cylinder. If you have not removed 4 nuts from the base of the cylinder, do not attempt to remove the cylinder, otherwise severe damage to the cylinder or engine cases is the only possible outcome of this.
What To Do When The Cylinder Is Stuck
Stuck Cylinders aren't all that uncommon, but there's also a way to address them so parts don't get damaged. Once you're certain all the cylinder base nuts are removed, and any power valve linkage is disconnected but the cylinder is stuck to the cases,
Do NOT Try to Force any Screwdrivers or Chisels Between the Cylinder and Engine Cases, Otherwise Damage to the Cylinder and Cases is Imminent.
It's not uncommon for cylinders to seize to the locating dowels and studs so anytime you're working with a stubborn cylinder, the best course of action is to spray penetrating oil on the cylinder studs, then allow sufficient time for the penetrating oil to work it's way in-between the cylinder studs and the cylinder before continuing.
Once the penetrating oil has soaked in, use a lead filled dead blow hammer and carefully strike the cylinder in an upwards direction while alternating sides until the cylinder is clear of the locating dowels, then carefully remove the cylinder from the piston while supporting the connecting rod and piston with your other hand so they don't crash into the cases once the piston is clear of the cylinder.
What To Inspect and Measure Once it's Apart
Once the cylinder is clear of the piston, take a quick visual inspection of everything looking for piston damage or metallic particles anywhere.
Provided there is no visible damage (ie: A Hole in the Piston or a Broken Piston)
and the bike ran before you took it apart we'll assume this is just a freshening up of normal wear items as the steps below will reflect.
If you've got visible damage (ie: A Hole in the Piston, A Broken Piston or Metallic Particles Everywhere), it's going to be necessary to remove all of the debris from the crankcase area and this is best accomplished by removing the engine and splitting the cases while replacing the bottom end bearings and seals as our article on splitting the cases illustrates.
For those that are just doing a top end rebuild for the sake of freshening it up, the following steps will have you replacing the piston and rings while eliminating any chances of putting it back together and having any problems so let's begin...
But First There's A Little More Disassembly
- Remove the Piston Circlip(s)
First ensure the bottom end is covered with a clean rag, then remove one or both of the piston circlips with a small pick, or with a pair of needle nose pliers while exercising caution that the circlip doesn't take flight.
- Push the Piston Pin Through
With one of the circlips removed from either side of the piston, using a small screwdriver try to carefully (so as to not gouge with the screwdriver), push the piston pin through to the other side.
What To Do If The Piston Pin is Stuck
Once one of the piston's circlips are removed, if the piston pin will not freely slide through to the other side of the piston and through the connecting rod with a gentle push from a small screwdriver, Do NOT Beat The Piston Pin Through To The Other Side.
If there is much resistance at all when attempting to remove the piston pin, it's essential that you use a piston pin puller, otherwise damage to the connecting rod and bearings is possible.
- Now Remove the Piston and Top End Bearing
Once the piston pin is out, you'll be able to remove the old piston from the connecting rod, followed by simply removing the needle bearing from the top of the connecting rod.
What Parts To Inspect for Wear in the Bottom End
Now that the top end is apart and the piston is off of the connecting rod, we can go over some of the common things you want to keep an eye out for so as to not have problems soon after getting it all back together.
- Inspect The Top Of The Rod And The Needle Bearing
Almost immediately after removing the piston pin, piston and bearing, it only makes sense to inspect the bore of the connecting rod's small end. What you want to be looking for is any signs of pitting or other irregular damage.
If any pitting or anomalies are noticed here, the connecting rod should be replaced. Additionally, even though you'll be replacing the top end needle bearing as it's part of your top end kit, be sure to inspect the old bearing for any signs of damage or missing needles as this will indicate there is likely going to be cylinder head and / or cylinder damage.
- How To Check the Rod Bearing for Wear
One of the first things most tech's like to do when they pull the cylinder off a bike with high hours is to check the connecting rod bottom end bearing.
This is simply done with the engine at TDC (Top Dead Center), with or without the piston installed by tightly gripping the connecting rod with your fingers and feeling for ANY movement UP or DOWN as the picture to the right illustrates.
Something Feeling Loose Down There?
It's important when checking the rod that you don't mistake any "Looseness" for side to side movement although if ANY movement is felt when attempting to gently pull upwards and push downwards on the rod (without turning or moving the crankshaft), the connecting rod bottom end bearing is shot and the motor is going to need to come out of the frame and the cases split so as to replace the connecting rod or crankshaft and rod as a pre-assembled and balanced assembly.
- Check the Rod Side Play
If the rod feels good up and down wise, (ZERO Movement) you'll want to check the side play and this is done by inserting a feeler gauge between the thrust washer(s) and the connecting rod and comparing the specifications to what can be found in a factory service manual specific to the motorcycle.
- Check the LH Crank Bearing
While the motorcycle is this far apart, it only makes sense to check the LH crank bearing and if you've never done this, fortunately there's a complete article on checking the left crank bearing on a 2 Stroke that's a must see.
Don't Forget about the Studs and Dowels
While the cylinder is off it is advisable to remove the studs from the cases as well as the dowels and inspect these for any rust or deformation, replacing any rusted studs and nuts or deformed dowels.
Note: When reinstalling the studs or dowels to the case, be sure to apply anti-seize to the threads where they enter the case, as well as apply a very light coating of anti-seize to the dowels before insertion.
Here's What to Look For in the Cylinder
Begin inspecting the cylinder (AKA Barrell or Jug), by removing any studs so the threads of the studs where they're threaded into the cylinder can be coated with anti-seize.
Next remove all of the other parts attached (Including the intake manifold and reeds if it's not case reed induction), as well as all of the powervalve pieces so they can be cleaned as this will better allow you to clean and inspect the bore of the cylinder for any scratches, gouging, cracks or other anomalies.
Powervalve's can be tricky if you don't have a factory service manual specific to the motorcycle as this is where they really come in handy.
If during disassembly you're unsure about anything, to avoid any problems upon reassembly, be sure to disassemble the powervalve while paying Close Attention to any timing and alignment marks or dots and lay all the pieces out exactly as they are removed.
The cylinder is an extremely precision part and in order for it to seal combustion gasses properly, it needs to be free of any irregular scratches or blemishes within the bore, along with it needs a proper crosshatch pattern on the cylinder walls to enable the piston rings to seal.
Over time the high and low points of these cross hatches wear and are covered over by combustion residue and burnt oil which doesn't allow the rings to seal properly and the engine begins to lose power, which coincidently brings us to right here.
Once the cylinder is clear of all the external pieces and all of the powervalve pieces have been removed, it's best to run a brush hone through the bore before inspecting it, then with a clean and dry cylinder, hold the cylinder up to a light source and look through it.
If there are any vertical scratches (or worse) in the cylinder bore, the cylinder must be repaired to work properly but there come differences in the way to handle this as it's important before going any further to determine if you have a plated or sleeved cylinder.
How Do I Know If I Have A Sleeve or Plated Cylinder?
Differentiating a plated from non-plated cast iron sleeve in some cylinders can be difficult to an untrained eye but if you place a magnet in the bore of the cylinder and it does NOT stick, this would indicate that you will be working with a plated cylinder. This means this cylinder has not been sleeved. However, There are cylinders which are plated, yet the magnet WILL stick but this is only due to the base material attracting the magnet.
Once you've determined whether or not the cylinder is plated, or has a sleeve in it you can begin to plan your strategy but there's really only two ways of repairing a damaged cylinder.
If you have a cylinder that is plated, the cylinder walls have a near diamond hard coating that is most likely a form of Nikasil (Nickel Silicon Carbide) or NiCom and retaining this bore is advantageous to boring the cylinder to accept a sleeve so you should forget about boring it and putting a sleeve in it and the following are some reasons why:
Boring a cylinder to accept a sleeve can cause a noticeable loss in power.
- Costs and Long Term Problems
Purchasing a sleeve and paying a machine shop to install it often costs more than replating, and adding insult to injury, sleeves can slip and turn in the bore negatively affecting the engine's power output!!
- Custom Modifications
Boring a cylinder to accept a sleeve will destroy any previously performed porting.
A plated cylinder maintains better lubricity and wears much slower and better than a sleeve, greatly extending time between service.
Bottom line is that boring a previously plated aluminum cylinder to accept a sleeve is effectively ruining a good cylinder (even with that huge gouge) as with a sleeve an engine will run hotter, may lose power, it'll wear out sooner, wipe out any porting and the list goes on...
For any damaged plated cylinder's, having the bore restored (gouges are welded, then bored) and the cylinder replated should be the only option for repairing OEM plated cylinders.
If you've got a cylinder which a magnet sticks to the bore, boring the cylinder is not the only option available as even a cylinder with a sleeve can be plated (Not recommended for aluminum cylinders which were previously plated but have since had a sleeve installed) but generally on sleeved cylinders, the common repair for these is an over bore to accept a new, oversize piston and this is an acceptable repair for sleeved cylinders such as those commonly found on older model dirt bikes.
The Cylinder Head
Inspecting the cylinder head for flatness with a precision straightedge is recommended, however, most people don't have a precision machinists straightedge so provided the motorcycle ran fine upon disassembly, and the top end is apart simply for the sake of freshening it up, the cylinder head should not need any attention other than a light cleaning of the combustion chamber and sealing surface, although do be sure to inspect the combustion chamber area for any signs of damage such as marks which appear as if the head was beat on with a pick axe as this type of damage is common when a needle bearing comes apart although you'd likely know about any such damage when you initially removed the head or when inspecting the rod and upper rod bearing as discussed above so we'll keep moving.
How To Reassemble The Top End
Cleanliness of all parts and mating surfaces is of utmost importance when going back together with the top end (or for any internal engine work) so allow me to point out a few things.
First make certain there's NO gasket material remaining on any of the sealing surfaces by using a razor blade and a piece of scotch brite on the end of your finger to remove any remaining gasket material from the sealing surfaces. (Note: During Cleaning of Parts, Do NOT Use A Rotary Tool, Otherwise Leaks May Develop.)
Next you'll want to ensure all the parts you'll be re-using are clean so it's wise to invest in a small parts washer (available at Auto Parts stores via special order) and wash all the parts which have been removed (Cylinder, Cylinder Head, Powervalve pieces, Nuts, Bolts, Brackets etc) followed by drying the parts with compressed air before continuing. (Do NOT Use Gasoline for Cleaning Parts)
Once all the parts are clean and free of gasket material, carbon buildup or other funk, place the cylinder on a clean surface, then while applying a light coating of 2 stroke oil to any moving pieces, reassemble the powervalve pieces exactly opposite of how you removed them, or as illustrated in a factory service manual specific to the motorcycle you're working on.
With Clean Parts and the Powervalve Assembled in the Cylinder...
Is That All The Help There Is With Reassembling the Power Valve?
Due to the complexities, and differences of powervalve's between manufacturers, this article cannot possibly cover all of the different arrangements, although a factory service manual specific to the motorcycle will provide exact assembly and adjustment details.
Next, ensure that the base of the cylinder and the top of the engine cases are clean by cleaning both surfaces once more with contact cleaner (or brake clean) and a clean rag, then install the studs and dowels (if removed) and place the base gasket over the studs while paying attention to the gasket's direction.
At this point you should be armed with a piston kit complete with gaskets, rings and the top end bearing, as well as you should have a clean cylinder that has been deglazed (honed) and inspected, or if your cylinder showed wear, you had it replated or bored and the powervalve should be reassembled at this point.
Now with all the other parts clean let's measure the piston ring end gap, assemble the piston to the rod and install the cylinder to the piston, then wrap this thing up.
How to Measure Piston Ring End Gap
Before installing the piston rings to the piston, it's critical that you first measure and if necessary, file the ring(s) to establish the proper piston ring end gap.
As the engine warms, the piston ring(s) will expand and once hot, if there is not sufficient end gap clearance the ring ends could butt against themselves causing immediate and costly piston and / or cylinder damage so don't ever install rings to a piston without checking the end gap beforehand.
Remember; You're only looking for a slight drag on the feeler gauge.
Should the ring end gap be too tight, clamp a fine file in a vise and working in one direction only, carefully file the ring end(s) until an acceptable end gap is established.
To measure each piston ring's end gap, insert a piston ring into the cylinder and square it up by pushing the crown of the piston against the ring until the ends are parallel to one another.
Once the ring is square in the bore, use a feeler gauge (available at any auto parts store) and check the clearance between the ends of the ring. (ring end gap)
Piston rings often come with an instruction sheet which will provide you with an acceptable ring end gap although if you don't have this, an acceptable ring end gap is .004" per 1 inch of bore. (Yes, Your Metric Bore will still measure in inches)
Now Let's Assemble the Piston
Begin by laying the piston on it's side on a soft cloth, then install either of the circlip's with your thumbs, then use a small screwdriver to ensure the circlip is in the groove squarely, and that the opening is facing up or down.
The need to install the circlip with the openings at either the top or bottom is imperative, otherwise centrifugal force could allow the circlip(s) to come out of their groove at high RPM's which only spells disaster.
Presuming you've established the ring end gap is adequate in a previous step and you've debured the end of the ring(s) and cleaned up any filings (if filing was required), inspect the rings for any markings which would denote "Up" (Anytime there is a marking on a piston ring, this indicates "Up") then install the ring(s) to the piston beginning with the bottom groove by placing one end of the ring in the groove nearest the locating pin and spiraling the ring on.
Now with one circlip installed, oil the top end bearing with the same 2 stroke oil that the motorcycle will be running, then install the bearing to the rod, followed by the piston with the rings installed and then a lightly oiled piston pin.
Make Absolutely Certain the Arrow on the Dome of the Piston
is Pointing Forward
Now install the other circlip using great care to ensure the circlip is squarely in it's groove and the ends facing up or down as discussed above.
Now Let's Get the Cylinder Back Onto the Piston
Finally, with the piston installed on the rod, coat the piston and rings with the same premix oil the motorcycle will be running, then coat the inside of the cylinder with the same oil.
Now with the piston and cylinder lubricated, locate the piston ring(s) to the locating pins within the ring grooves and using your fingers, compress the rings, then using your other hand, carefully guide the cylinder straight down over the piston until the base of the cylinder meets the top of the cases.
Note: Some models are a real PITA to get the rings compressed and into the cylinder with the piston on the rod. On these you may find it easier to install the piston and rings into the cylinder before connecting the piston to the rod, then install the piston hanging half out of the cylinder as an assembly onto the rod, finally installing the piston pin and circlip before lowering the cylinder.
Once the cylinder is flush to the cases, while using a diagonal pattern in steps, if necessary, use the proper torque wrench adapter (these are available at auto parts stores via special order) and be sure to torque the cylinder base nuts to the proper torque as can be found in an OEM service manual specific to the motorcycle.
Next, with the cylinder securely bolted down, ensure the top of the cylinder, as well as the sealing surface of the cylinder head is clean by cleaning each once more with brake clean and a new rag, then install the head gasket (which may be o-rings) followed by the cylinder head, any sealing washers and finally the nuts which must be torqued per the specifications found in a service manual specific to the motorcycle.
Finally reassemble and adjust any external powervalve linkage, then reassemble the remainder of the motorcycle while being sure that the coolant is properly refilled and bled, the air filter is properly serviced and that the intake boot gets put back on properly otherwise you'll be doing all this again soon!!
How To Break In A New Top End
Properly breaking in a new top end is really easy... All you need to do is place the bike on a stand then start the engine and allow it to run at a low speed (just keep it running) until it has fully warmed up (~15 minutes), then allow the engine to cool fully and repeat this process for a total of 3 times.
After this break in process, the bike should be ready to ride normally.