Your procedure sounds good. My guess is the pulsating is from pad transfer of some sort, which is slightly odd since you're using new rotors though (perfectly fine to reuse pads with new rotors, I am on my Evo). My suggestion is to remove the rotors and sand them by hand with some 120-grit until the surface looks shiny again. Try to do this evenly across all friction surfaces of the rotor. Also use the 120-grit to take a small layer off the face of the brake pads. This will give everything a virgin surface for bedding together.
Follow these bed-in procedures:
http://www.racingbrake.com/v/main/te...in%20procedure
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