Can't do the main bearings or rear main seal with the transmission attached.... for that pull the engine.
Pulling the pan with the engine in the car isn't hard (been there done that). Personally, I'd recommend just pulling it, but I've had it off with the engine in the car and the wire harness all still connected. I have no idea what your problem is; you've just got to get the front of the engine elevated a dozen inches or so (I think it was closer to 8") and you don't even need to pull any cross members. Is your engine swinging forward as you lift it? Do you have a leveler?
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