Hey,
I believe the frames are pretty much different on the 96+ bikes. Your best bet would be to get a Vortip or Thumper Racing baffle. Bajadesigns.com has both for ~$70. They help with power, while only increasing noise output a little. For ~$220, Xrsonly.com has their Competition Exhaust pipes (tunable Supertrapp) that do very well in my opinion. I've got one on my '87 XR200, and '96 XR400. They are quite a bit louder than stock with all the discs installed, but with a fewer disks, it gets quieter, at the expense of power. Furthermore, they will recommend jetting for your bike with the pipe that will be pretty much right on. At lower speeds, the pipe is not obnoxious. It puts out a deep, throaty thump. At higher speeds it starts to scream, but nothing near the obnoxious noise 2-strokes put out.
Pulling out your existing baffle is an option, but you will have to rejet yourself. The Vortip or Thumper baffle would be my choice if I was on a budget, and Bajadesigns will probably give you a ballpark for jetting. If you have some $ to spend, go for the XR's Only pipe, it looks sweet, sounds sweet, it's tunable for noise vs. HP, and it (with the jetting) does alot for throttle response and overall HP. Good luck, and keep on thumpin'!