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My driver's door glass was smashed to steal my GPS . It's a '95 F250. I took the glass from an '85 and it rolls up fine till about half way then it gets really tight. I removed all the glass out of the weatherstrip and the electric window motor worked great before so what happened? On LMC truck's site they break out the years 80-86 and 87-96. The roller on the bottom track is different and the track on the 95 is made a little different, but nothing I would think that affects function. I did notice that the division bar between the vent window and door glass is wider on the '95 than the '85. Did they change the width of the window glass?
It could just be the rubber seal in the front track is pulled out a little now... guessing you dropped the vent window to install the new glass? Maybe try loosening the vent window assembly and put the main window up before you TQ it down.