I am not sure about this. When I was putting my YJ together, I was having problems shifting my NP231. I couldn't shift it by "hand" at all. I called up JB Conversions who specialize in these transfer cases and he told me that you couldn't shift it by hand from underneath. What I am thinking is, do you think your internals are so loose that they are jamming up once it is together? My brand new NP231 doesn't shift by "hand" at all... that is why I am thinking something is "falling" out of sync, maybe just enough to be a wedge.
Check out "YJ V6 Conversion" if you want to see a frame up restoration of my 1992 YJ.
Check out "WWII Jeep Photos AND Restoration of..." if you want to see the original JEEP in action...