When I install a manual transmission, after getting it started, I get two "guide bolts", longer than the housing bolts bolted onto the two top bolt positions near the cylinder head to guide it in. Then, I lay under the car and sort of bench press it and slide it toward the motor along the path of the aforementioned guide bolts. It might help to install some guide bolts at the top near the head and then lay under and try to bench press it and slide it out. I have to do that to properly line up the transmission shaft with the center of the clutch but if you have separated the tc from the flex plate, it should be able to come out without all of that effort. Is the transmission hitting the side of the car somewhere, preventing it from being pulled away from the motor? Maybe, if you disconnect all motor mounts and put a jack under the motor, you could lower the entire powerplant to pull the tranny out.