Sometimes the one from the old pump stays on the tube. Sounds like you are on top of that. I don't understand how there can be no water making it into the motor.
The only thing that makes any sense would be the top grommet getting fouled. You can force a hose onto the tube and the hose pressure should force water thru the system. That would eliminate a blockage above the pump. On the bright side your lower removal and install times should be greatly improved.

