Theres two ways to do it. If you want to use your stock forks to keep the cost down:
Since the 99-03 R1s have 298mm rotors and a 6 bolt pattern, if you want to mount 04 or newer wheels(04-06 R1 have 320mm rotors and 5 bolt pattern rotors) on your bike you can use 03-04 R6 rotors which are 298mm and have a 5 bolt pattern or just buy an 03-04 R6 front wheel complete with rotors. The only other thing you would need to do to fit the wheel is use washers to space the calipers inward about 1mm. What you do is use washers between the fork and caliper.
Or you can change the entire front end, forks, calipers etc... You can keep your stock triples, axle, and the fender will fit.
The Rear fits without modification on an 02-03, use the 04+ caliper and cush drive, and use the 02-03 spacers. 99-01 have larger rear rotors so, you need to use the caliper and caliper mount from an 02-03 for the rear to fit.
I've done both methods on my 02. I first fit the wheels with stock forks, then decided to upgrade to 04+ forks, calipers, and rotors...

Since the 99-03 R1s have 298mm rotors and a 6 bolt pattern, if you want to mount 04 or newer wheels(04-06 R1 have 320mm rotors and 5 bolt pattern rotors) on your bike you can use 03-04 R6 rotors which are 298mm and have a 5 bolt pattern or just buy an 03-04 R6 front wheel complete with rotors. The only other thing you would need to do to fit the wheel is use washers to space the calipers inward about 1mm. What you do is use washers between the fork and caliper.
Or you can change the entire front end, forks, calipers etc... You can keep your stock triples, axle, and the fender will fit.
The Rear fits without modification on an 02-03, use the 04+ caliper and cush drive, and use the 02-03 spacers. 99-01 have larger rear rotors so, you need to use the caliper and caliper mount from an 02-03 for the rear to fit.
I've done both methods on my 02. I first fit the wheels with stock forks, then decided to upgrade to 04+ forks, calipers, and rotors...
