I'd pull the engine. It makes life so much easier when you have the engine out of the car. Everything needs to remain clean, and it is a much larger task to do so if the engine is still in the car.
Think of it this way, to remove the engine you would have to:
remove wiring
remove axles
remove mounts
remove shift linkage
disconnect all hoses, vacuum lines
to do this in the car you would have to:
remove cylinder head (which means almost all wiring and accessories)
remove transmission to get the flywheel off and get to the crank
remove axles and linkage to get at the transmission
its basically the same job, except with the engine in the car you will definitely be struggling, or it won't get done properly.
the choice is yours, this is just my input.