Just wanted to update what I hope is the end to this saga:
Just got my truck back for what I hope will be the last time. Went to a second dealership, and it was night and day difference in the service (also probably helped that GM exec's were aware of what was going on). But man, it gave me hope that there are at least a few good techs out there that can do the job properly.
They replaced my replacement window because the glass guy at the original dealership didn't seal it correctly. It is still the FAYUO 43R-000042 window, so that hasn't changed. The paint has been taken care of. The headliner looks l like new. They cleaned up the mess of caulk left by the original caulk job. Overall, they did an amazing job but it took forever and a day and some conversations with the right people to make it happen.
Now the big test is this week - storms 90% and above for the next 5 days. Praying it doesn't leak again, but so far this morning it has been solid.
I guess the moral of the story is, if you don't get a good vibe from the first dealer, don't be afraid to run like hell to another one.