Install the vent windows in the doors, but leave them loose. I leave the adjusters out at this point (the threaded allen head driven pieces with the wide flat integral washers). Install the door glass, then add the adjusters and set the vent into correct place. You won't get the door glass in if the vent is fully seated first. As far as the quarter glass- install the glass with the track first, then the regulator unit. it's a pita, but more time consuming than difficult.
Thanks. The door glass never came out, just got taped up for painting. As I recal the only issue with them was getting them past the weld nut that is behind the large mounting hole. The rear quarters I just remember them consuming a lot of time and trial and error getting them out.