GM warranty? Is it because you bought it at a GM dealership or something?
Anyway, there are a bunch of posts on this type of stuff. Supposedly, if you revert to the stock tune and drive 50 miles, it'll erase the aftermarket tune from your car's memory. However, some say that Ford can always detect whether the tune has been changed or not. I think it comes down to how strict a dealership wants to be. I'm not sure how different extended warranties are from factory warranties though...
If you plan on taking it to the dealer after using an aftermarket tune, try switching to stock tune. But I would assume your warranty is at risk.
1988 GT - Stock
*SOLD* 2012 GT Premium, Black on Black, 3.55 Axle, HID and Security Package, Pypes Pype Bomb Axle Backs