I went through the same trouble shooting when I tried to isolate the cause of my HU doing the same thing...long story short..scrap the factory amp...it was the only thing that solved it for me.Spent a good part of the day checking some grounds. Found the one to the intake manifold was cracked and very corroded, so I spliced in a new section and got rid of the connector. Also found that the nut and washer on the positive stud of my alternator were corroded or damaged by excessive heat, probably caused by poor contact with the oversized wire lug I used when I upgraded my alternator. Also found that one of ground wires on the PS inner fender had busted and corroded wires, so I replaced that ring terminal. Also found that the nut on the positive stud of my aux battery terminal was loose. What a mess, but at the end of the day after all the fixes, I still have the hum/whine. I even pulled out all of the fuses, and no change, except of course when I pulled the radio fuse. I even ran a ground wire from where the amp is grounded to the extra gnd wire I tapped into that goes to the HU. Still have the hum/whine, do l'm guessing it is due to the amp for some reason. Will try the ground loop isolator as a last resort, and if that doesn't work, I will have to bypass the amp. What a cluster and waste of time...