I usually completely disassemble my engines and check the fits. The key item is to get the crankshaft to spin freely in the case when all is super clean and dry.
I have a 5x40 x 1” bolt from which the head has been removed that I use for many tasks. Call it the "stud".
First, I remove the cylinder and piston and backplate from the engine. Screw the stud into the crankshaft, put the rear of the engine on a wood block, and give the stud a whack with a hammer to drive the shaft out of the Drive Washer.
Next is a step you only use for non-anodized case engines! Lap the shaft into the case with toothpaste, or 1200 grit valve compound. Clean VERY thoroughly (I use an ultrasonic cleaner and (gun) bore brushes) You want all that stuff OUT before you run the engine, or it will never stop cutting!
If the case is anodized, you have to polish the crank down to fit without touching the case. The anodizing provides a hard, oil absorbant finish you don’t want to remove.
Chuck the stud into a drill or drillpress, screw the shaft onto it, and at medium speed, polish the crankshaft surface. This is done by wrapping a piece of well oiled 600 or finer w/d paper around the shaft in a loop where you are holding both ends pinched between your thumb and forefinger. Run the paper up and down, and also get the front face of the crank-web. Just a half minute should give the surface an incredible shine. This reduces out of roundness, wavieness, and improves surface finish. This was something I tested with Cox's QC equipment, so the effect is real.
Now, I go a bit farther, and rebalance the shaft. I grind flats from the crankpin boss to the edge of the "smile" counterweight. Then I drill a 1/16" hole down the center of the crankpin to just above where the conrod bearing area ends. Thus the crankpin root is at full strength, and no durability is lost.
Finally, I will take my Dremel with a small diamond bit and smooth the rear edge of the "window" port in the shaft to smooth the corner where the incoming charge transitions from the venturi to the crankshaft hole. This is inside the crank, and you probably should wrap the shaft in masking tape to prevent slip-ups from touching the outside of the shaft.
The rest of the engine is left stock, unless the piston/cylinder fit is unusually tight. If so, you have the opportunity to add a bit of taper to the piston and cylinder. I do that by hand. Again wrap some oiled 600 grit around the top half of the piston, and rotate it by hand, moving the paper slowly upward. Two or three shots of this should reduce the top diameter by about .0001". Similarly, use 600 grit on a dowel to open up the cylinder from about 1/2 the bore downward with special emphasis below the top of the exhaust ports.
Ideally, the piston should now go easily to about 1/16" below the top of the bore and then stop (Again with everything ultra clean and dry).
Use an ultra-sonic cleaner and brushes and towels to get all the grit and grinding debris out of the engine. I reassemble mine with Tri-flow teflon impregnated oil. May help, may not.
Use the stud with a 5x40 nut and a couple of oiled washers to pull the drive washer back onto the shaft. Try to start it into the old grooves, and make sure it bottoms out.
For comparison, on a stock 6x3 Cox gray prop and 30% Nitro, my Medallion .049 turns 16,500. My best Tee Dee would do 19,500 on that combo. Good luck. 
Larry Renger
think S.M.A.L.L.