Yup... ya pointed out all the pitfalls of doing it one piece at a time, Bob. Could get lucky and have all line up first go... not unheard of.
It really ~IS~ easier to put the trans up to the engine and bolt it all together on the floor first, then slot it all in as a unit.
I've done it one-two numerous times. I've done it as a unit dozens, if not 100+ times. I will avoid pulling/replacing one at a time like th' proverbial plague. Even with a "pilot shaft" things can go downhill. I use a worn input shaft as a clutch alignment tool and have still had things go sideways.