I just bought a V6 mustang and was very interested in modifying it with new exhaust as well. When I mention this to my brother, who just so happens to be a car salesmen, he warned me that if I do any modifications to the car that are not installed directly by the car company it would void the warranty. He suggested to me that I talk to somebody from the dealership that I bought it from and they could install some ford made dual exhaust and pretty much anything else that I wanted to "tweak." I would suggest that you do the same if you are worried about the warranty.
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