When window is fully up the door won’t close. I did a bit of stuff that needed to be addressed. Can’t seem to pinpoint the window adjustment causing this. It will close when the window isn’t fully in the up position. Any ideas?

 

I would slowly shut the door and compare the reveal of the glass around the weather stripping to the other side of the car. That should give you an indication to how it is out of adjustment.

The shbox instructions are the pathway to getting things right. (The factory doesn't even have a procedure, but shbox is solid on this!)