I S/M'ed a 2000 Xr650R a few years ago:
Light kit from Baja Designs (that made it street legal).
Wheels from Central Wheels in Britain. You can barely fit a 5.0 wide on the rear but don't bother - get a 4.25 with a 150 tire. Or was that max 4.25 but get the 3.50? Can't remember now! I had a 160 rear for a while and was too round on the rim and I never used the whole tire. The 150 lays down a bigger contact patch. Front's a basic 120.
Brakes I never quite got dialed in - your master cylinder isn't up to the task of a tackling a decent 300 mm disk (OK for the easy street use, but fades out pretty quick). You really want to get a decent 2 or 3 hole caliper, and a master to handle it.
Engine work: You must, must, must uncork the carb. Honda Power-up kit is cheap and worth it. Pipe (I had a Big Gun) dumps a ton of weight, but gets pretty noisy.