I took my 2005 GT to the dealer a few times for minor concerns after I had my CAI, tune, UDP's, Eibach springs, and the rear end gears shanged out, I had no problems with turning it in for warranty work because the items that I had issues with had nothing to do with the modifications I made to my car.
I have heard all kinds if horror stories about people that had bolt on mods and how their dealer's service department would not service their vehicle because of it. I say "find another dealer" Any reputable dealer that wants your business will honor the manufacturers warranty as long as your mod's are not directly responsible for the issue you are having
Good Luck..
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