Are you using a transmission jack? Try letting most of the pressure off the jack then get under and twist back and forth, (you may have to play around with the jack in small increments) I've also removed the jack and got under the transmission with my head toward the engine and used my knees to lift while rocking the transmission back and forth and toward the flywheel at the same time, or even grab the rear of the transmission and lift up and down while pushing. (I take it you are not on a lift). Whatever you do make sure you get it fully seated and do not try and draw it up with bell housing bolts, and make sure the Jeep is solid on your stands before manhandling the transmission. Put some extra crap under there so if it falls it can't fall all the way.