If it's under warranty then make sure you get new rotors AND new pads. Not aware of any problems on the Mustangs, but this is a BIG problem on the Super Duty trucks (at least early 2000 era). Contrary to most folks' belief, the rotors are not "warping", you're getting pad material thermally transferred to the rotors, creating high spots on the rotor. You can have them turned down, but if it's a warranty repair, have them put new ones on.
However you fix them, the best single thing you can do to get good life from your brakes is to properly "bed" your pads. Do a Google search. It's nothing more than a series of near stops to heat and cool the pads and rotors; the key is to not stop for any time with hot rotors and pads (this is a good practice even after you've bedded them). If you've gotten them hot, and you're stuck at a stoplight, creep a little so that the pads are not sitting in one place on the rotors cooking.
FWIW, I'd be happy with 30k on a set of pads and rotors if I'm driving hard.
Also, my personal advice: Don't spend your money on drilled rotors; slotted rotors add some value but all of my research indicates that drilled ones are more prone to cracking, and don't add a lot of value, at least not on street cars.
