I thought you meant unplugged from the RCA connectors. Do you mean completely undoing the wiring?

A good chassis ground connection is lower impedance than any wire. Very close to the amp is good, but running a a ground wire from the amp to the iPod is not as good as a chassis connection.

The noise eliminator might help Does it install on the alternator or in series with the electronics? Still think you might need continuous shielding on the cable as well as inside the changer.

 

Only when it's on

 

Got a new ground loop isolator from PAC: Amazon.com: PAC SNI1 Noise Isolator: Automotive

And connected its ground to the bolt bolting down the amp/cd changer rack. Problem solved. Next up I want to try to remove it from the signal path and just do the grounding

I've also received a power line ground loop isolator I could try, which i'd like better since it wouldnt be in the signal path.