Several things come to mind immediately.
Harmonic balancer and flywheel. Same as the ones in it before?
Drive line, same one?
If the driveline has bottomed out on the splines from using the wrong driveshsaft, it will have a fierce vibration.
I agree with your decision to separate the motor and pump.
Is there a chance there is a rock or rats nest in the pump? You would be shocked.