You can do it.
All of the stuff that we've all mentioned is stuff to be considered.
Your gearboxes are in great shape; if
@orangefj45 rebuilt this stuff, it's unquestionable.
If you *want* to replace the clutch and rear main seal while you're in there, great (and I would... since you're in there... especially if you don't know the condition of it - if you were driving it with this clutch before, just run it, you'll know where it is and how to change it later if you need to).
Getting a gearbox and txfr on an engine that is in the vehicle is just a matter of geometry. Jack it up, or lift it with an engine hoist extended in through a door, or use some ratchet straps or a chain hoist on a 2x4 across the doors,... there are a dozen ways to finagle a gearbox/input shaft into the clutch/flywheel. It might be annoying, but it's totally doable.
Guys who work on trans/txfr cases do not pull the engine to get the gearboxes out. It's doable. People remove their transfer cases from the trans from under the truck. Again, doable. Get after it. You'll be happy when that input shaft slides into the pilot bearing!
Good luck,
TDC.-