I have the same issue, I replaced my McIntosh with a JVC R820BT, I now I have a terrible alternator whine. When the key is switched to just accessories ON there's no noise. But when you turn the whole car electrical system on, or start the car the noise is there and fluctuates with the RPM of the motor. I've tried using my phones audio output to run a signal into the RCA cables that bring the signal into the amp and this gets rid of the noise so it's definitely the head unit and not the amp or cabling harness. But I'm not sure what to do next, I might try putting an alternator noise suppressor between the battery and alternator, but this seems like a hack solution to me.