I am wishing you the best. I think you may have answered your self. Bolt troubles can be initiated by unleveled pieces that will not come apart. Can you get 2 jacks? One under each component? They have to be pretty level to seperate.
I would start all over. I would put the other bolts back in, level the tranny and motor. Then I would attempt to take out the trouble bolts before the other bolts.
Is the setup out of the car? I wouldn't take out the tranny inside the engine bay unless I had a jack under the motor and a "tranny" jack under the tranny. It is not safe to do this without support. If you only have one jack shimmy up the motor with blocks etc. level with the tranny - then use the jack for the tranny.
Good luck. RFT