Did you clean the rust of the hub where the rotor sits? I'm doing that soon in hopes of solving my pulsation.
See my car was fine until it needed new back brakes. Well I had it done at the school I go to. They replaced wheel cylinder/shoes/drums and hardware kit. For some reason they turned the front rotors even though it wasnt pulsating. Ever since then it has pulsated badly. Well I replaced the front rotors twice and new pads once, and replaced the back drums with ones from NAPA pulsation still hasnt gone away.
The pulsation isnt as bad now, sometimes it is worse than others.