I fitted 2003 R6 wheels to my 2003 Gen1. Both wheels have the same rim size so tyre size is the same.
front wheel is a straight swap, except for the discs, as the later Yam wheels are 5 disc bolt fitting rather than 6 as on the Gen 1s.
Rear wheel takes the Gen 1 sprocket carrier and spacer so the left side of the rear wheel is OK. The Brake side needs some more thought and at least one extra wheel spacer.
I ended up using a GEN 2 ABS rear caliper and carrier that I modified with a welded plate to match the Gen1 torque arm. I needed a different rear disc (again 5 vs 6 bolt fixing) and i think i ended up with a Gen 2 rear disc as well.