Here's the list so far of what I know will/will not swap.
WILL SWAP:
Wheels (front & rear)
Rotors (front & rear)
Sprocket Carrier & Cush drive
Gearing
Gas tank
Fuel pump
Clutch cover
Alternator cover
Rearsets (both sides)
Rear brake lever
Shift lever
Shock
Fairing stay
Tank cowl
Front master cylinder & lever
Clutch lever
Throttle assy
WILL NOT SWAP
Forks
Front brake calipers
Triples (top & bottom)
Front fender
Ignition* (could be made to work, but the 03/04 has one extra line for security. the 05 doesn't have this)
Axles
Battery tray / rear heat shield
AFTER MARKET STUFF
* Power commander from an 03/04 will work *** I talked to Dynojet and they said that if you are using an 03/04 on an 05, you *must* have it custom mapped or it won't map right. I don't know why, but this is what they have told me. The firmware is different as well.
* Scotts damper - Scotts is in the process of making a new mounting kit as the clearances are different. Per Scott "the 03/04 might fit, but with clearance differences, I wouldn't recommend anyone try it".
* Exhaust systems will fit, but the mounting points are different for the headers and at the tail, so you will have to fool around with it and possibly fabricate a few brackets.
More to come...