I found it to be silly things like the afore mentioned aircon pipe hooking up on things and preventing the flywheel from turning when undoing and tightening clutch bolts.
Getting the box on again is fun. Lift, wiggle, (doh, me arms are aching)....relax. Then repeat until it slides on. You'll probably need to lower the gearbox end of the engine tilting it down to aid removal.
You got an engine support to go on the top of the wings?