As long as your rectified (DC) charging system doesn't exceed 12.8V, you can use any 3 cell lipo battery.
Any battery will fry if hooked up to an AC system, so be sure that you're hooking it up to the rectified portion of the system.
You can simply substitute the HID and lead battery with the LED and lipo battery on Kennerz' or Rogue's wiring schematics.
If your charging system exceeds 12.8V, you'll damage the battery, so be sure that your voltage regulator is working (it should keep it right around 12V).
If it doesn't, then you'll have to go with a lead battery or a lifepo (lithium iron) battery...they'll handle a standard 14.8V charging system.
The lifepo batteries are heavier and a bit more expensive than lipo batteries, but they're extremely durable in comparison and have a higher working voltage due to cell voltage differences.
They're the same "lipo" batteries that are on the market now for quads and streetbikes, so that makes sourcing a big enough battery pretty easy.