If I remember correctly, The awd transfer cases use a 5-bolt pattern unlike the 6-bolt pattern on 4wd transfer cases, This will be the biggest issue with trying to use stock transmissions and transfer cases. -UPDATE: Appears it is a 6 bolt flange so that isnt an issue, Im guessing the problem is the input spline count wouldnt match? You should be able to disassemble and swap input to fit 32 spline manual output shaft.
I did an nv3500 manual transmission swap on my 2003 Suburban 4wd. Got rid of the 246 A4WD and replaced it with a 241C from behind a 4L80E since it has the same output spline as NV3500/4500. Did no tuning im happy with how it runs sometimes it high idles when coming to a rolling stop in neutral but slows down after a second at 0kmh