OutbackV2008,
Do you have the identical situation as Jeff with the noise in only one zone?
Is the noise high-pitched alternator whine, only with the engine running, changes with RPM, always at the same level regardless of the volume level?
Is the HU a Kenwood?
Have you removed the HU power & ground wiring entirely from the factory harness and redirected those connections at the same point as the amplifiers' primary terminals?
Is ALL, 100%, of the audio equipment getting power and ground from the same supply/battery/etc. ?