I won't quote since my head isn't quite working good enough...

Whine:
I believe the problem is possibly not power through the empeg. For testing I've had the empeg powered off the cigarette lighter socket. I was still getting the whine with the tuner AND the tape deck though, so the noise must be getting into the amp somehow. I'm still going to try running of the Ibus supply but I'm guessing the CD changer has some special circuitry. It appears from the diagrams I have that the CD changer outputs balanced signals. I have a few things to try first (after power from Ibus)

Isolator:
A ground loop isolator goes on the RCA audio lines. The whine is coming from currents flowing through the shields in the RCA jacks. Filters can be placed on power lines, but the problem is caused by the loop through the audio circuitry so start there. The isolation transformer is a special 1:1 audio transformer. I managed to pick one that was reasonable quality for A$20. Disdavantages are that they generally roll off at high and low frequencies (particularly low if I'm thinking right)

Lag:
Now that I think about it, my debugging showed the empeg received the button commands instantly and it was the software that was slow. So maybe it's not our code