Not saying that you don't need new brakes and rotors, but have you made some hard stops with the heavy load to help true the rotors. Mine would pulsate if I was driving unloaded for a while. I would hook up the trailer and do some harder braking and it would fix it.
If not, powerslots and hawk pads are a common recommendation.
2002 f-350 PSD, 4x4, cc short bed, 6spd, ccv mod, airdog, AIS filter, isspro ev and scangauges, detroit TT, ITP boost annihalator, ITP RR, bellowed up-pipes, ats housing, turbomaster, 3.5 dp magnaflow, very happy with ultra smooth and linear PHP 50t, 80DD and "whisper" tunes.