Think about it; the position that the drive shaft is installed should not matter. The drive shaft is balanced as a unit, it is not balanced with the trans or the rear diff. What you do have to consider is the "clocking" of the u-joints. If you drive shaft is such that removing it can change the relationship between the u-joints, then your method of resolving your viberation issue should work. If both u-joints are attached to the drive shaft, then I would thing there is something else wrong.
So some questions:
Did it viberate before it was removed?
Did you change anything on the drive shaft?
Did you change anything else that could cause the viberation?
