I'm hoping to be able to tap into the wealth of information that is NICO.

1994 Nissan Hardbody. I want to replace the 4 speed auto with a 5 or 6 speed auto. Any ideas?

The 5 speed from another hardbody should be a direct swap. You'll have to punch a hole in the firewall for the clutch master and such, but I imagine its well documented.
A 6 speed on the other hand may be a bit more tricky. You could try finding one from an S15 Silvia and swapping bell housings... anything past that and you're going to need to make custom trans mounts, adapters, drive shafts, etc.