Just because your T5 got rebuilt doesn't mean its not the problem. The main shaft could be bent, in fact most of the time when they are in a car that gets beat on at the track, they do end up a little bent.
Describe the vibration better. Does it vibrate hard, or is it a light vibration. There will always be a slight vibration especially with an after market shifter.
An aluminum drive shaft will only help if the original drive shaft is the part that is out of balance.
ShortThrow50, don't throw away that trans, send it to me.