Merry Christmas, 6XCHEVY,
The one advantage of doing it as you describe, is that you do not need to open/disconnect the torque-tube connection.
Yes, alignment of the transmission front/pilot shaft to the clutch is a consideration. There are a variety of ways to deal with this. Here are two ways:
I look at this as a 2-person job (maybe someone will correct/clarify).
1. put the transmission in neutral
- remove the inspection cover from under the clutch housing
- "jimmy"/rotate the flywheel to align clutch to front/pilot shaft (using a prybar or large screwdriver or rotator tool in the teeth of the flywheel)
2. put the transmission in gear
- raise the rear of the truck and put stands under the truck (first: chock both sides of a front wheel)
- have a friend/spouse rotate a rear wheel (and hope it rotates the drive shaft)
If your u-joint cover is leaking, you might as well remove the transmission (get a gasket/seal kit and follow the adjustment instructions in the Shop Manual).
If my logic is faulty/unclear, someone will correct this.
Good luck.
Well stated Tim. Especially the part about if the u-joint cover is leaking. The OP should be hoping that his is leaking so that he will have reason to do the swap the easier way (install engine with transmission attached to bell housing).
Carl