Good info to know....
I do know on my old Tacoma after removing the driveshaft to do something else, and re-installing it, I picked up a vibration. I had to take it back off and rotate it 180 degrees in the yoke on the axle and it went away. Same driveshaft, and same rear end, but apparently I upset the "zen" of it being mounted one way for its entire life. When I move it 180 out the first time, it didnt like it. Hard to understand why it did that, but it did. Just a thought.
It also seems if the shaft is a little (key word little) longer, it would be better as it is shoved farther into the transfer case and is now supperted even better by having more spline contact. (assuming you dont have a SYE here....) Did you pull the shaft all the way out of the transfer case? If so, maybe the splines are not back in the exact same spot and have a different wear/twist and causing the vibe? (really stretching here though....)
Good luck with it.
~James