I've been running a 2004 frame for 6 years now. the font wheel is 40mm further back and the head angle goes from 28.5 degrees down to I think 26.5 or so (not sure but will check).
it puts plenty of extra weight on the front wheel and some of the last factory racers had the headstock then moved forwards (at the new angle) 5-15mm in order to increase the wheelbase and balance the weight a little more towards the rear.
the other change is of course the coil mount. pre '04s had SEM and '04+ had Kokusan so the early coil must be mounted on its side but it is easy.
fitting the separate regulator and rectifier from 2002 was easy to fit and the combined 2003 item goes under the seat anyway....
the handling is far better. the triple clamps need to go to 18s and this finishes the job.