...For the most part, people dont realize both the internals of 03/04 and 05/06 are identical. The only real upgrade are the radial brakes and the weight distribution of inverted forks (Less mass in an upward/downward direction means less tiring/more controllable bumps) however even for myself, these are negligible.
Before commiting to the 05/06 upgrade, i took my friends 06 for a test drive. With both completely stock suspension minus the proper setup for each our weights, both reacted identical on the street; from 250kmh straights to sharp 100kmh right handers and so forth, there was no noticable difference. Considering the ergonomics of both bikes are nearly identical, the only real difference i could pick up was braking strength which i'd assume is due to the radial brakes on the newer bikes. However after installing my double-H EBC pads along with my goodridge SS lines, i must say the feel just as flawless.
So in reality, all this mod is accomplishing is a cleaner, more modern looking bike.. If the price is right, and your forks are either finished or completely stock, then why not. But if you're running race internals set to your proper weight and youre comfortable on the bike, by all means continue to ride it! Sell your bike when it comes time and buy a bike 2007+ with the newer Showa systems and then there is something to compare to (Stiffer, completely rebuilt dampening system, much more track oriented).
Sorry to rain on the parade; i still do believe it looks 100x better than the conventional forks on the 03/04, however it is not a necessity, and anyone with properly setup suspension will be utterly disappointed with the mod's outcome.