have you considered sticking calipers and/or brake pad retaining pins?
someone on this site or another, who does a lot of car work apparently, was 'stuck' on this for awhile, so it may not be readily apparent even to those who do alot of brake work. (btw, i don't know that he had your symptoms, specifically).
another possibility, however remote, is a blocked or partially blocked brake hose/line.
in my experience, pulsating seems almost always related to rotor or bearing issues, but since you have done that work, i suggest the above as outside possibilities.
btw, when you got the new rotors, did you check, or have them checked, for run-out? it wouldn't be the first time that new rotors were out of spec.
//bc