1999 to 2007 Supersports are pretty much all the same except for transmission and engine.
I have some carbon Fiber slip-ons (Marving) for sale locally, if you pick up the shipping I'll send them your way. here's the ad:
1999 and Up Ducati slip-ons
Other than a bigger moter, you can't do anything else, the slip-ons aren't going to do much but they will sound awesome. Even the slightly larger 800 only has 75hp. If you want straight line speed, ditch the Duc and get a liter bike.
The hot ticket for the late model budget supersports are:
lighter wheels from the 1000DS or 2003 800 Supersport
aluminum box section rear swing arm from a 900SS
or ultimately the aluminum swing arm from the 2003 800 Supersport or any 1000DS
Adjustable forks from a 2003 800 Supersport or 900/1000 Supersport, ST models may fit too.
Better tuned Rear shock.
Drop to a 14 tooth front sprocket or go up a few in the rear.
Slip-ons.
Superbike forks up front if you want some bling, but your better off with bolt-ons from another SS.