One way to do it, which is a PITA, but may end up being shorter - is to hotwire the whole Empeg up. Run your power and ground leads staright to the battery. Droop your cables over the seats to the amps, etc. At this point you should have NO alternator whine. Now, hook these items one by one back up to the way you have them now, and something should suddenly make it come back.

I generally rewire all my cars from scratch. The only time I had alternator whine was with a bad ground... I had a CD player grounded to a vary large piece of metal, and assumed that was good enough. It turned out the metal was a structural part of the dashboard, and was actually isolated from the frame of the car by some large plastic bumpers (to keep noise and vibration down). Anyhow, that piece of metal I grounded too was not actually a "ground". Instead the CD player grounded itself through the RCA cables to the amp!

Good luck -