There is different rear linkage (CR copy) on the 04', and it has Showa suspension. The motor had some basic refinements with porting and headwork and the standard jetting was cleaned up dramatically over the 03'. The changes are definatley noticeable in stock form, and many praise the return to Showa suspension. I say the 03' should be substantially less or go for the 04'.
Things to watch for: bent linkage bolts (04'), bad crank bearings (replace at first signs of flywheel play), do not over tighten rear axle nut, better to use a castle nut and cotter pin. Clutch overheats if rode hard, you can increase oiling by adding more holes inside cutch hub, and slightly raising oil level. Stay on spokes when new, they loosen alot. Oem hardware is not the greatest, use a torque wrench or be careful. These bikes tend to be hard on reeds, check if low end response gets wierd. Shifting can get notchy, shift forks wear quickly. Keep the ignition area behind the cover cleaned after washing and watch for oil residue from bad left crankseal.
Don't let any of this scare you, the bikes are great performers. Just know what you have and maintain it.