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Sounds like you may have some bad rotors. I am assuming you had them turned due to being warped. I would see about replacing them under warranty since you only have 3500 miles on the truck. The rotors shouldn't warp in that amount of time unless you are riding your brakes. Good Luck!
I have an 04 screw I just had the rotors replaced on mine .The milage at the time of replacement was around 11000.They only turned them once and replaced them on the second trip to the dealer, no problems so far.
I told my dealer I would pick my truck up to day ,and that I wont'ed the service manger to give me a statement stating my truck would be safe to drive,they said ford would not let them do this. Thats when I started raising hell.They called me back and said my truck would be ready in 3 hours with new rotors. I have bought 18 fords from this dealer in from 1969 till now.I have never had to play hard ball befor.I like my 04 F-150 but what a pain in the ***
Catfish Mike - Good on you for sticking to your guns. A lot of the time it isn't the dealer, it's Ford. When the dealer does warranty work they have to get approval just like those crazy HMO's we have to deal with. Anyway, good luck with your truck. I know I have been greatly satisfied with mine. Happy New Year to you!
JC