im in the process of dropping in an engine - and right now im in the prep stages (before the actual drop in). the question is short, sweet and goes like this - do i have to remove/drop the transmission for the drop in ? a 302 block is going in, nothing custom about the setup.
Personally, I never pull a motor on these cars without the trans still bolted to it. Betting the trans mounted up to the block is much easier on the ground than in the car.
Some folks will leave the trans in place though, it isn't required.
It sounds like you have the motor out and the trans is still in the car? I would leave the trans where it is and deal with lining things up later.
i think it is easier to install the motor with the tranny at the same time. makes it easier to line up the clutch and what not while it is hanging in the air, rather than fighting it from under the car. if you are auto i dunno, but a 5 speed or manual tranny, this is the way to go. if you are doing both at the same time, jack the back of the car as high as you can safely.
i have done it both ways. i would lean to the side of engine and tranny as an assembly. it installs pretty easily and no underside work for clutch/trans alignment as jerryD said. it works out both ways.
auto trans.... engine disconnected from trans is the way to go. takes a little more effort to line up the flexplate to torque converter but is way easier than engine/auto trans combo install