Did you remove the shift drum before you attempted to remove the transmission?
I only needed a flywheel puller tp split my cases. I used some of the longer bolts from the cases, threaded them into the holes near the dowel pins, and used a plastic mallet to hammer on the bolts. This drove the cases apart. For reassembly, to install the crank, I heated the bearing inner race on the right side a bit with the torch and the crank dropped right in, by gravity. I installed the seals after assembling the case halves.