Well it appears they fixed it. It goes up and down with no tilt now, but it's really slow and REALLY slow at the top. Also, the rubber on the top of the door panel that runs along the glass now flips under when the window goes down. Maybe due to the shop moving the glass closer? Not sure, but at least I can tint the windows now. Here are some pictures on how they repaired it.
(This is the passenger door)
Before:
Bottom right track after shimming:
Top right track after shimming:
New metal glass mounting brackets from Isuzu:
This is how the guides seat now:
Any suggestions to keep the top rubber gasket from buckling under?