A jet kit and high-flow filter never hurt anything (at least, not properly installed...).
Installing a Supertrapp slipon on my '93 made a huge difference in how freely the engine would rev, I definatly recommend loosing the ugly stock can!
You can change the performance characteristics of the bike by changing sprockets as well. Larger in the rear means less top end speed, but more accelleration, smaller in the rear means less accelleration but more speed (I may have this backwards...).