"The reason I am considering separating the two is to have shorter and lighter pieces to line up."
I'd say good idea in concept, but the execution will not go well. It's tougher to line up the od to the gearbox than to install the whole M41 unit.

It's difficult, heavy and awkward job when laying on your back and the car is on stands. A couple of things I do...
Get the car as high as practical. I think I've had mine on concrete blocks under the tires.
Use a clutch alignment tool when installing the clutch - it'll make the trans. installation go easier.
Keep the gearbox in 4th as stated earlier.
You may want to consider something like this transmission jack. http://www.harborfreight.com/450-lb-low-lift-transmission-jack-61232.html
I bought one years ago. Although it doesn't make the job "simple", at least it carries the weight of the transmission. Still takes some fiddling to get the trans mated up to the bell housing.

Just be patient and don't force anything. It's amazing how easy everything fits together when it's all lined up properly.
--
"Differences of opinions should be tolerated, but not if they're too different' - Sharon Craig