I didn't pull the transmission back, but took the engine out instead, so my experience isn't 100% applicable here. However, rusty dowel pins were the main source of my frustrations and it wasn't until we had opened the gap enough to fit a pry bar in there that things really started moving.
Since you have already backed the transmission off a bit I would wager the pins aren't what is holding you up. Are you sure you've disconnected the shift linkage and the pitch stopper?
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