I am not recommending this, try it at your own risk!
An even sketchier trick, but sometimes works, is to put tension between the engine and trans with a ratchet strap and then shake the hell out of it. If you have tiny misalignment, the shaking corrects it and the strap tension pulls stuff together.
In general though, given your description, I would pull the engine out and verify everything before trying again.
You will probably find rubbing marks somewhere that identify the problem.
Most of the time I have this issue it is because the tranny is slightly nose down and the engine is slightly nose up. Figure out how to pivot the front of tranny up slightly, sometimes as little as 1/8 or - 1/4” does the trick. Maybe have someone pull down on the tail shaft housing?