Give the setting tape several days to really lock the glass in tight. After 24 hours, you can handle the parts, but it takes days to really lock in. With the proper thickness setting tape, you should be able to easily mate the glass to the channel. Only slight tapping with a rubber mallet is necessary. If too difficult then the setting tape is too thick. The tape the common vendors sell is much too thick for any part of the truck.
I cant really remember, but I believe I used 1/32" thick tape for both door glass and vent windows. Went together easily and locked tight after several days.