I just replaced the rear rotors on my '05 GT- 13,000 miles- I got a pulsation at the pedal, and knowing that Ford doesn't cover rotors under warranty, I took it to a past Ford technician who now has his own shop.
The rear rotors were the problem, but were too thin to machine. He suspects poor material. The pads at both ends, as well as the front rotors were fine.
I will now take it up with Ford. My mechanic said that the original rotors were now "changed", due to "issues" (from the Ford dealer where he got the replacements).
Apparently there IS a problem. Now- to uncover it and get the cost of the rotors re-imbursed.