If you mean modifying the stock muffler, I wouldn't bother with that.
Everybody seems to be using the FMF Q4 muffler around here, and a lot of those riders also use the FMF Powerbomb header along with it.
As long as you install one of the electronic fuel injection programmers AS WELL, along with disabling the airbox inlet flapper AS WELL, you'll get a very nice increase in power and throttle response, oui, oui.
I also recommend lowering the final drive ratio quite a bit, but everyone seems to have a different opinion on that one. :)