Haha well I guess it's time to update a little bit.
New amp came in. The whine and noise is still present, but is better than before. It's obviously a ground loop now, and I'm working on tracing it. The problem with the previous amp turned out to be a blown component to the rear speakers. I must say my sound it a lot more full-bodied now
Methodmann0666 and I are currently working on revamping the entire setup, not the least of which will be checking all the grounds and power leads from the alternator. I'm also going to try a little different strategy for grounding the whole thing, we'll see how it works out.
We've already installed my new Yellow Top battery and the fibreglassing work on the new subwoofer enclosure will continue this weekend. The new additions to the car are a Focal Power 1.800 amplifier and a Focal 27V2 subwoofer. It'll be getting 600W at 2 ohms in a nice sealed enclosure.
I'll post up some pictures of the progress next week!