When I removed my transmission, the engine wanted to tip forward and the transmission wanted to tip backwards, causing them to get into a bind. It seems like there was an alignment pin on either side of the transmission that bound up. Also, the input shaft could bind up if the engine and transmission are not aligned. Try propping the front of the engine up with a 2x4 to keep it from tilting forward. Make sure the transmission is aligned with the engine, and it should pull apart.
Good luck!
Steve