[SubieNubie]

Update:

Hopefully this saves some leg work or solves a problem for someone else.

I've traced my grounding issue back to the amplifer. I tried powering the amplifier on power and ground off my power wire and ground, I ran already for my AudioControl LC2i line out converter, in lieu of off the factory amplifier harness. But it did not eliminate the issue. Given that I ordered an Alpine MRV-F300 to replace the Alpine KTP-445U. It gives you more power and more flexibility in a slightly bigger foot print. Its also has the ability for high level inputs, and its about the same price as a KTP-445U used on ebay. In addition to this I found a review on Sonic Electronix that also addresses an issue with alternator whine when using a line out converter with the KTP-445U.

After I swapped that in, I tried utilizing the factory amplifier power harness to power my LC2i. But the a grounding issue reappeared. So as of now the only thing I am running off the factory amplifier wiring harness is the speaker inputs to my LC2i and my speaker output to my woofers in the doors, thats it. The output is crystal clear, no static what so ever.