If it was my bike the first thing I would do would be to feel the brake tracks on both wheels with my fingers. If the rims feel noticeably concave, that's brake wear. I'd be reluctant to put the time it takes to rebuild a wheel into that rim.
Since it sounds like you have already decided to rebuild the wheel set, the next thing that I would do would be to disassemble both wheels. Measure a spoke from each side of both wheels and write down those numbers someplace. Measure from the inside of the elbow to the end of the spoke.
Now completely disassemble both wheels. When they're apart, lay them down on something flat to see how warped the rims are. The flatter and rounder your rim, the easier the rebuilding process will be. If the brake tracks are worn, of if the rim is very warped, I wouldn't bother with it. If you decide to replace the rims, the easiest way to determine spoke length is to find exact replacement rims. You may be able to find brand new replacements, but I doubt it. Otherwise you are going to need to find and figure out how to use a spoke calc program.
Good luck. If you decide to proceed beyond this point, post again with whatever questions you have as they come up.
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