Please help with alternator whine in speakers and popping noise when powering on/off.

[aod]

Hello all,

My audio project for my 1990 ZR1 has been a nightmare. I sent my speakers to Dr. Don to have him fix the amps in them because they were dead. Excellent service and turn around time, by the way. Next I wanted to upgrade the head unit so I went with a Pioneer Appradio 2 so I can also hook my Android phone to the head unit and get hands free bluetooth in the car along with navigation from my phone and pandora for tunes. The idea was to not cut or mess with any factory wiring and retain the original bose speakers with the upgraded head unit. I ordered the unit through Crutchfield and they included a harness that let me do just that. This is the harness:
http://www.crutchfield.com/p_1207018...r.html?tp=3486

Everything went together fairly well, all except the 14' of cable in a run where you really only need about 2 or 3 feet. Anyhow, I get alternator noise and some ignition noise along with loud pops when powering the head unit on and off. I've tried everything Crutchfield has told me: Grounding to a good ground - as a test I even ran the ground directly to the battery. This did not help. They also suggested cutting the wire ties off the harness and fanning the RCA cables away from the power wires, which is probably something they should have done in the first place. Anyhow, this did not help the issue either. As a test I would remove one RCA cable from the head unit one at a time and when I did, the alternator whine in that corresponding speaker actually got louder. To make certain that it wasn't the speakers, amps, or something wrong with the car I removed the Metra wiring harness and re-connected the factory wiring, then connected the stock head unit back into the system. There is no noise whatsoever when I do that, so that limits the problem to either the new head unit or the harness. Crutchfield is sending me out a new head unit and harness which should arrive in a couple of days. Somehow I am not convinced this is going to solve the problem. If it doesn't, does anyone else have any ideas on what to try? I'm guessing I'll probably end up with RCA ground loop isolator filters but I'm already at capacity inside the dash even after cutting the old support for the bose head unit out of there.

Thank you much for any help in advance!