Hello,
I pulled my trans off of the engine first, but I took mine all apart. If the trans input shaft is not stuck try using a couple of jacks to change the engine and/or trans angle. They may just be binding on each other. Sometimes just the slightest change and they slip apart, so jack a little and try, wiggle a little,etc.. An extra set of hands is a big help. Good luck ,let us know what works.
Gary