Status Update: Problem Solved (so far, so good)
The new alternator didn't solve the problem,

so I start looking elsewhere. After a long time of searching and no luck with finding bad wiring, I finally decided to pull the "radio" fuse and let it sit. And I'll be dang, no dead battery.
Now just so, everyone is on the same page. I have the Bose radio and it is supplied by two circuits. The "radio" circuit is a 10A circuit and only supplies the "switched" 12V. The other circuit is the "Amp" circuit, it's rated for 20A, and supplies the "constant" 12V.
So my problem was with the switched 12V circuit, which totally surprised me. After looking at the schematic, this circuit has to runs. One that goes straight to the radio and the other goes straight to the OnStar unit in the trunk. Once again a dismantle my dash to get to the wiring and nothing looks questionable. So I decided to rewire everything and see what happens. At this time I decided to just hack the harness and take out all the "
Factory System Adapters". Got it all done, everything working good. Put a DMM on the battery at got 12.4ish volts, let it sit overnight, got up this morning and still had 12.4ish volts.
So I'm thinking the problem was in the wiring of the System Adapters, which was a PIA to fit behind the dash anyways. I don't really feel bad about not using them, because I got them free as part of some promotion. But you would think they would have a little better QC. I assumed they were good and they were what causing me problems the whole time. Oh well, lesson learned.