Bill and Wilbur mentioned the two keys to getting the windows in with ease. When I reinstalled the corners in my 54 I used a squirt bottle with a strong dish soap solution. The rubber needed to be "massaged" so I took an old toothbrush, cut off the end, touched it to the disc sander to put an angle on the end. About the same as a fat straight-slot screwdriver. You can lift the rubber without scuffing your paint.
BTW...This little home-made tool has gotten a workout during the entire rebuild process. I've noticed Eastwood offers a complete set but I'll stick with ole "Oral-B."
Using this soapy solution, some mechanics gloves for grip and the little tool the windows went in without any problem. Hope this helps!