Micki you'd be surprised how flexible our warranty is.
If you do a mod, obviously the mod isn't covered. If something else breaks and they can prove the mod did it, then that won't be covered either.
Other than that, its all good.
Say you got headers and your engine failed. They'd have to somehow prove it was the header's fault (they can't just say 'you modded your engine, its your fault'). They'd probably try to but you could fight it.
So good luck!
Some ideas: Exhaust, wheels, coil-overs.