The 4L80-E/NP-241 transfer case to trans bolt pattern is identical to that used by the Allison/NVG-263 (at least the gasket is the same - I've used them interchangeably). I don't know if the trans output shaft is the same (diameter, # of splines, depth, etc)....

You should be able to use a manual shift transfer case. In fact they are/were optional in the 2001+ trucks. The wiring harness is different - due the lack of stuff on the manual version. I don't know for sure, but an electric shift wiring harness might work for a manual shift Txfer case - you'd just have some unused connectors.

Jim