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The most important thing is to match your pistons to the cylinders. The cylinders were stamped with a number at the factory. That number tells you the diameter of the cylinder.At www.biker.net you will find the Yamaha Service Manual. You need to read the part where it talks about cylinders and pistons.
If the cylinder has never been used (NOS), then the factory cross-hatching is as new, and you do not want to use a hone on it. A hone would damage the cross-hatching. Try using some light oil to soak into the rust and see if it will wipe clean.
You would have to measure the diameter of the pistons, you plan to use, to see if they are compatible with the cylinders you have. The piston to cylinder clearance is very important.
After you read the Service Manual you can ask more questions, if needed.
NOS use wet (sprayed with rust remover) steelwool to remove rust DO NOT HONE, BORE or otherwise screw up a factory upset, match pistons to bores and go from there... the bore will clean itself