For starters don't use the factory ground for either the empeg nor the other head unit. Find a place on the floor of the car under where you have the heads mounted. Hopefully somewhere where there's already a bolt of some sort. Remove that bolt and sand/grind any paint/finish off the metal surface. Put some loop terminals onto the ends of your ground wires and make sure they touch that bare metal - put the bolt back to hold it tight.

Next is trying a different interconnect between your empeg and stock unit. Try a shorter length and different type of interconnect. I just used CAT5-e UTP for mine (1 pair of wires for left and 1 pair for right - the other two pairs unused - everything mended nicely with heat-shrink tubing).

Bruno