As I said in post 5, the alignment is good. All within specs. They checked the transfer case too, see post 9. I did talk to them a couple days ago and they are going to send the removed pinion yoke with the driveshaft to the balance shop so they can check it with and without it.
I wish I knew someone close that had a 2007-2008 truck like mine to swap their driveshaft into my truck for a test run. From what I have found, in 2009 they changed something on the driveshaft as the factory part number is different.