To measure the clearance, check the bore of the cylinder with a bore gage and then measure the piston diameter. The difference is normally .001-.003 depending on the engine builder. If you go with .001 you really need to warm up the motor before riding to prevent cold siezures, .003 is about stock for my 03 CR250 and you can barely warm it up and ride with that clearance. Anything over .005 will lessen ring life and may require push starting.
Also remember the piston usually wears more around the skirt, so if the top is fine, the bottom may be out of spec.
Stan