The best initial bang for the buck will be a pipe, air filter, and jet kit. I was able to find a listing for an air filter at Rocky Mountain ATV, but the only jet kit I found was a Dial-A-Jet. DynoJet doesn't seem to list one. K&N might but I haven't found it.
For a pipe, your best bet is probably a Universal model of the SuperTrapp IDS2 or similar.
To do more than that, you're better off boring the motor, or just getting a faster quad.
Rob