I've been doing some reading on this, working on my own ATV. I have a model with the Rotax 1000 engine.
The engine itself probably shouldn't be the only thing upgraded. Consider the clutch. It would need to be either adjusted or upgraded in order to get the power from the engine to the drivetrain. Axles are another part that can be upgraded to thicker, heavier aftermarket parts.
I would start reading stuff from performance vendors. The ones I've mentioned below have been happy to answer every question I've asked.
MrRPM- Big Bore kits, race heads, intakes, cams
Dynojet- Engine tuning modules, Autotune add-ons, LCD displays
SuperATV- Loads of different stuff
CanAmPartsGuy- More good stuff
Demon Axles- Several grades of axles
Good luck with your build!
Mark