This does not sound too cool. I wonder if one of the flex couplings is out of balance? It should be a standard quality control thing to balance check them in manufacturing.
You have to go back and line up the driveshafts exactly on the same splines before even looking there. One spline out does not sound like much but I just do not know. Also have a look to see you did not accidently knock off a factory shaft balance weight.