Do you have a local machine shop that does boring and honing?
Your cylinders likely aren't perfectly round due to wear. Even though they might look good, we're talking 1000's of an inch so you won't be able to tell without measuring with the proper (very precise) tools.
Once they measure your cylinder, they may say "it just needs a hone" but more likely you will need to bore the cylinder oversize (thus making it perfectly round and matching the size precisely to the new oversized piston, which the machinist will use to determine the exact size to bore the cylinder out.
So, take cylinders to machinist, have him measure. If it needs to be bored, ask him how much oversize it needs to be (a lot of the time mine have had to go straight to .5 over as the wear was too much for .25 to cover), and then buy the appropriate piston and take it to the machinist with the cylinder, and he will bore the cylinder to match that piston.
Make sense?