Since connecting the Empeg with the AC adapter eliminated the whine. I would assume that you are getting the noise at the empeg unit and wouldn't mess around with your amps any further.

When you have the empeg on AC power, is it out of the dash? Perhaps you only get the noise when the unit is in the dash and the wires are all compressed together. This would be inductive interference or a stretching of the wires at the docking connector.

Perhaps you don't have a good ground at the empeg unit or the power leads are coming from a bad source like close to the ignition coil. This should occur whether the unit is in the dash or not but on battery power.

I get noise when the unit is in the dash only. I haven't quite figured out how to eliminate it except for removing the unit from the dash. I can duplicate the noise by putting some of the wires close to the unit or to each other. I need to play around with it more but it hasn't bothered me quite enough.