A couple of my Empeg installs have have had ground loops that were notoriously difficult to remove.

To help diagnose the problem, try grounding your RCA cables where they go into the amp (aligator clips, wire & tape...whatever...it's just temporary). In every case I've had so far, the loop was between the empeg and the amp. If the noise goes away when you do that, you know that the empeg is not grounded properly. Make sure you double check the sled harness connector to make sure you're getting a good connection (some had dodgy crimps). I'd resolder that pin just to be sure.