OK - I think I can actually answer this one, maybe Jesse too. Anyway, I have been weighing everything I pull off and everything I put on both to satisfy my OCD and to actually see what the numbers are.
50 lb reduction will be very difficult and keep the bike street legal. The big weight droppers are the exhaust and battery, but here's a brief break-down of what I've found so far (net reduction in weight):
Replace full exhaust (Akra, Yosh) will drop about 10 lbs.
Replace stocker with LiPo battery: 5. Those are the easy ones.
Replace bars with Clip-ons: 2.5 or so
Sato or similar rearsets: about a pound
Remove Passenger Peg - left side (right needed to mount muffler) - a pound
Remove Passenger Seat - about 3 lb.
Remove Mirrors about 3/4 lb each.
You get out of the realm of street legal with removal of these:
Kickstand assy: 2.7
Headlight assy: 5 lb
Signals, horn, cali-can/smog pump, left side controls, factory bodywork, all that stuff came off the race bike. Right now, not including the weight of race bodywork, a stripped-down, and definitely not street-legal R3 is 55.7 lbs under the weight as delivered by the dealer. If I'm lucky, I'll be close to 50 under when all is complete.
EDIT: As it turns out, I only got 45 lbs. under stock weight:
http://www.r3-forums.com/forum/753-yamaha-r3-garage-build-area/39585-does-your-r3-need-diet.html