Skat Trak Impeller
I have owned a 96 Challenger for the last 6 years. I've made a few mods and probably the best mods for me were a 14.5/22.5 Skat Trak impeller (the 17/22 works well too, but I prefer the 14.5/22.5) and Nauticus Trim Tabs (these made a tremendous improvement in all around ride quality...almost completely illiminates porpoising and chine walking and much quicker to plane...Nauticus claims that you may see a 1-3 mph gain in top speed due to the hull working more efficiently...I can't say that I noticed that, but I didn't lose any top speed either) these won't make your boat sound better or faster, but sure will make it more pleasant to blast around in.
I agree with Phildoo, these Rotax motors seem to be very near their performance/power limit right from the factory and that aftermarket flame arrestors, tuned pipes, water boxes, etc...only add minor performance improvements. I think you'll get better performance gains by modifying your pump and fitting it with a quality impeller and not the OEM 11/25 impeller with square leading edges, if you haven't already. In my opinion the stock impeller (11/25 pitch with straight leading edges as opposed to tear drop/rounded leading egdes) is junk and should be replaced. My experience with the stock impeller was that I had to walk the boat out of the hole unless I wanted to cavitate before hooking up and getting on plane...Skat Trak impellers have been far superior for me, both the 17/22 and the 14.5/22.5 worked well for me. Hammer 'em out of the hole and your up on plane and gone...no cavitation!