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On my D3 setup I have both the GMCO and the HU grounded to the stock radio ground wire, and they're both powered by the hot wire in the stock radio plug, but I also have a noise filter connected to those power wires and two ground loop isolators on the HU RCA outputs. No whine in my setup
It's also possible your problem could be due to the way you have the amp power wires and the RCA's run, or the way the amp power or ground is connected.
Do some experimenting and answer these questions for us....
Do you have any whine if you use the radio without the engine running?
Do you have any whine with the engine running and the radio on but the volume muted (rev the engine a few times)?
Does the whine change pitch with the RPM of the engine?
Does the whine change pitch depending on how loud you play the radio (constant RPM)?