I concure with most of the info posted by others.
If you removed the drive shaft as an assembly by simply unbolting it from the differential yoke at the 2 U bolts lowering it and sliding it out of the rear of the tranny housing and did not remove the universal joints from the drive shaft. I can't imagine any reason for completely removing a front or rear u joint just to drop a drive shaft for a quick-ee speed-o gear swap? Chances are, the shaft assembly balance is not altered and the shaft can be re-intalled without regard to it's "clocking" to the rear yoke.(180 degrees either position)
Next, drive shafts are in fact balanced and generally have small steel weights welded along their surface. Generally, shafts are balanced at a machine shop without the universal joints attached. Unless the shaft has been bent, twisted, crushed, shortened, lengthend or lost it's weights, or has a thick layer of undercoating applied to one side it will remain balanced.
I would suspect based upon your information provided that the vibration that magically occured after removing the shaft is in fact a problem with the universal joint at the point of disconnect. You have either not ensured that the u joint bearing caps were not properly seated in the yoke journal or you have installed the bearing cap/s with missing or misplaced needle bearings. Re-check the u joint at the point of disconnect make sure all bearings are in place and the u joint caps seat in the indent of the differential yoke fully. Make sure to torque the u bolts evenly and to the specs.
