Here is something i wanna share with you. I hd a 96 I30, bose HU died and i boguth an alpine HU. For the life of me, i used the rca metra harness, i could not get rid of the whine. WHINE WHINE WHINE, it was terrible. i troubleshot like you did, all this stuff, making sure grounds were good, this and that and had no solution.
Obviously the stock radios whether it be a bose clarion or not are designed to eliminate the whine by either isolating it with a built in isolator or actually removing the ground loop. My thoughts were that it was the power antenna on mine as well despite the fact that i trashed in in a car wash and had to remove the whole module. Granted, the car was older, who knows how all the wiring actually aged, regardless of that, i wound up purchasing 2 ground loop isolators from
http://www.partsexpress.com and it solvd my issue, well hid the issue.
Unless an electrical engineer can explain how ground loops happen and whatt he viable and most likely sources are in a car we are left guessing and trying to fix it on our own. Some are able to solve whine because something was bad on the alt or grounds weren't good, fact is a car is quite complicated, alot of nooks and crannies and with more and more electronics being put into new cars it makes it that much more difficult.
I hate to say it though, you may not fix this and isolators may be the answer, you can try and try and try but it may not be worth the effort of changing wires and grounds and in doing so possibly messing up other things. I am all for doing things full and proper and isolators are a good and easy way to eliminate whine most of the time but it may be the only solution. Hope this helps and makes you feel a lil better that there are those out there siffering from whine, Good luck