This is kind of weird to me. To be honest, I didn't know anybody would put an engine in and have the tranny already mounted to truck. I really don't see why and I would never do it. Bolt them together on the floor or bolt the tranny up after engine install. Both are way easier and no risk.
I have done this with both 3-speed and 4-speed enclosed drive-shaft transmissions.
Why?: This saved me the work/parts/gaskets/gasket-adjustment/time needed to re-attach the u-joint and the enclosed drive-shaft ball/bell/cover.
It has been a while since I have done this - but, I think that I/we (I needed a helper) had the rear-end on stands and the transmission in gear - one of us could rotate the transmission front-shaft (main-drive shaft) by rotating a rear wheel (to get the front-shaft lined up with the splines in the clutch plate).
I used two alignment "pins" (one in the clutch housing attached to the engine and one on the transmission).
Would I do this if the transmission was out of the truck, attached to nothing? No.
