Spincycle,
Good advice for you from everyone here, especially Sundog's comment about sorting pistons. When I was building a lot of Yamahas back 20-30 years ago, I would typically stock 50+ pistons, and I kept them all sorted on actual/measured size, not "marked" size. They do wander up and down a bit (and also vary in taper as well, which can be just as important). And it's totally possible to freshen an engine a number of times and stay on the same pistons size!
As far as the quality of the bore -- as long as you go to someone that has experience honing (and preferably uses a floor model Sunnen hone and uses a "keyway mandrel"), you can and should get excellent results. It's *always* good to have the header (or a dummy header), and a top deck torque plate on the cylinder while honing. Tightening the header will distort the cylinder out of round, and the top plate (fake cylinder head) will turn the top of the bore into a bit of a "stop-sign" shape. Don't over-tighten header! Keep the torque very low, and double nut them to keep things from coming loose.
PM