I am not sure I believe the transfer case thing. The late model 3rd gen troopers use the same transfer case as us and there are tons of those in the yards. I would just do a 5 speed swap if you are that worried.
I have been running manual hubs for 4 years, cross country drive, I regularly wheel the old girl with a front locker to boot, and I have no problems.
JoeD put a manual transfer case in his VX, so it is easily doable.
Good luck!