The warranty should cover original parts; if you replace a part and it fails, obviously that's not covered, but if that failure causes a downstream problem (i.e. change intake, and a piston gets screwed from stray dust) then you're on your own for the downstream damage. Basically consider it, "If the car's owner hadn't changed part X, would part Y (which failed) have failed?" If I read the warranty correctly, they won't void your entire warranty, just the part that you tinkered with.