You could try measuring the DC earth voltage at both the empeg and the amplifier with an accurate voltmeter, relative to the battery - terminal. This should be done with the engine on and the system playing. If you have more than a few mV voltage difference, you may have a bad ground somewhere. What swg wire was used for the power & earth wiring? Did you look at grounding the bonnet across one of the hinges with a flexible braided strap? What sort of ignition leads do you have? You could try changing to resistively-suppressed ignition leads.

I have to confess I have had real trouble getting rid of noise in both BMW and VW before now, even with just an ordinary radio and a complete, dealer-supplied suppression kit.