Welcome Doug!

Where are you from? (just a city or zip code)
I would have said the transmission input is not entering the crankshaft pilot bush, but you say that the dummy shaft (alignment tool) slips all the way in, and it would be obvious if the gearbox shaft had a bigger pilot than the tool. 💡
I'm not super familiar with the NP gearboxes, so I'm going to suggest that you create a new topic on the main page, where more people will see it than in this obscure corner of the New Members section.
Once again, thanks for becoming a member of our little community!
Jim,
Lil'Red is a '87 F250 HD, 4.10's, 1356 4x4, Zf-5, 3G, PMGR, Saginaw PS, desmogged with a Holley 80508 and Performer intake.
Too much other stuff to mention.