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From what I believe it will void the warranty if it is to be the cause of the problem!
My buddy Joe just had some Kooks w/Hiflow cats and X-Pipe installed on his '04 so if a warranty issue comes up we'll find out!
But I don't think it will unless it is the cause plus if you put on Headers you will need to have it Dyno Tuned and this will be an issue with the stock tune at the Dealer.
Their computers will put it back to stock but later you will be able to go back to the Dyno shop and they can re-install the Dyno tune!
It's a process but well worth it Joe's '04 pulled a 353 RWHP run 3 times and about 367 RWTQ after the tune and Headers!