[Bladerunner]

Calipers would work ok, and for most things, they are real handy. But in my experience the cheaper digital calipers were very hit and miss, you might get a good set that was very accurate, or get one that gave you a different measurement every time. We bought about 12 pair of different types in the shop i worked in, and only found one that gave reliable results, but we considered it a fluke because 2 of the same brand were flakey. Calipers as a general rule are supposed to be accurate within +-.002, and even though those read to a resolution of .0005, if ylou look at the paperwork you get with them, they will usually say "accurate to within .002" my digital mitutoyo calipers are the only exception I have seen to that, and they only claimed accuracy of +-.001 they also cost $176, so take that for what it's worth.
Your service limit (total allowable wear on piston to cylinder wall clearance) has a variance of only .0013 which I would not depend on calipers to measure dependably.
You seem to be approaching this project methodically, and that attitude will give you a much higher success rate, and far better quality of workmanship than diving right in and having to backtrack when things don't turn out right. The mic set I showed you will be far more accurate, and using the plunger set, you can measure not only the top, but the middle and bottom of the cylinder as well (as outlined in the manual)..you do have the shop manual downloaded? if not, get it, it is really the best tool you will have, (besides your ability to take things one step at a time, and do the best you can, not shortcutting yourself)
all that being said, if you don't know how to read a mic, it can be kinda tricky, there are many resources online to help you, of if you know a machinist, they can show you as well. Or as has been suggested, taking it to a shop where they have all the tools and letting them do it is a great idea, I was assuming you wanted to have the tools to do it yourself, but if you don't plan on doing more than a few rebuilds, this may be the better option.