This adds substantially more annoying noise (harddrive, processor, etc), regardless of whether the empeg's line level output is connected to the head unit or not.

The very first thing I'd try is to upgrade the stock harness ground (didn't see you try that) - heavier gauge and to a known good ground point (sand away any paint so you get down to clean metal against the ring connector on the wire). Snip the ground wire immediately after (1.5-22 or so) the plug/socket on the car harness, attach your heavier wire there. No harm done to any stock things...

/Michael