UPDATE: It was the BCM that was damaged due to water intrusion due to an incorrectly installed windshield. I ended up taking it to the dealer to have them deal with it, because this late in the game, as a single daddy with an 80-mile round-trip to work every day, I needed my truck to be solid and reliable.
Where I originally was looking at the door harness seals for water leaks, it turned out those connections were good. I'd have never expected my windshield to have been the cause. You get those installed and figure the guy knows what he's doing.
The work order came out to just over $1000. A guy was to come and reseal the windshield, and all was supposed to be well. Then I got a call saying the windshield was going to break upon removal (most likely), and I'd need a new one installed. Work order just jumped up to $1300. After some "discussions" the dealer was able to knock a few hundred off the labor, bringing me back around $1000 to fix everything, All in all, I missed two days of work due to the truck being down, which probably brings the loss right back up to $1500, but such is life. I'm just hoping we are good to go from here. I'm usually really good with preventative maintenance and making sure problems don't get super expensive, but I didn't even see this one coming!