When the time comes to replace my motor and tranny, what options are there?

Can a 44RE be replaced with a 46RE?

Can you swap out an auto for a manual? How much work would it be?

Ultimately I would like to go from my 5.2L w/ auto 44RE to a 5.9L w/ manual (NV3500 I think). I have also thought about staying with the 5.2L, but still going manual if possible. I don't want to have to re-invent the wheel to get there though.

Someone has to know something about this.