just commenting in case it is helpful...
lastdan: im not sure if youve already passed this hurdle but, have you eliminated the empeg as the source of the sound? ie, just wanted to suggest running the RCA cables from the empeg, off to a portable stereo or home stereo, and see if the whine is picked up there (ive done this to troubleshoot my own unit, parked in garage and run RCAs to my room to listen to the output) it will at least tell you if the loop is coming from the empeg, or elsewhere (amp wiring)...?
justin: if youre not getting alternator whine (or other electrical interference) then i dont think it is a ground loop issue? just my first thought - going on wild goose chases ripping up ones dash is no fun, as i know