Just want to update this in case anyone has this issue in the future, however unlikely.
I dropped it off at the dealer Monday. They didn't get to working on out until Tuesday. After 4 days of diagnostic (including swapping the BCM with no luck) they were able to trace the problem to a broken ground wire in the A pillar. Apparently that was causing a strange power feed back to the BCM causing the issue with the window and door lock.
I got lucky since I can return the window regulator and BCM I bought. I'm only out the very fair labor cost the dealer charged me considering it took them days to diagnose.
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