There are "loop holes" that the dealer can refuse to do a warranty job but they "never" do refuse to do it. The only problem I would see is the ehaust work. They may have you pay a small fee if the aftermarket exhaust requires more work to get the tranny out. We had a F150 that was supercharged and needed a head gasket replacement, the customer had to pay for the time it took the tech to remove and replace the unit down to the intake. I hope this helps. Tony