I'm sorry that I'm just getting back to this. The dealer and I had a little argument over something else when I was in for previous work (not window related), so I am not sure how or who is paying the for the window, but I just dropped the truck off and a whole new assembly is being installed. Slider, glass pieces, etc. I will get more info when I get the truck.
I really pressed them on the caulk fix, since they are a high volume Vette dealer, I asked if their Vette customers would allow that to be a repair that they would be okay with.
It stinks how many different answers everyone is getting. I hope they take pics of the cracks.