Nevermind. Figured it out. I popped the window sliders out from the scissor arms so I could move the window manually and then tilted the window forward until I had enough clearance to place it back in the tracks. Took a bit of persuasion but I finally got it. Window now works fine.
The sliders look pretty bad however so I'll be picking some up from the dealer tomorrow.
BTW how hard is it to fix the door stop? The sheetmetal around the stop is all broken off so I'm thinking body shop that can weld a new piece in place.