Good troubleshooting! You probably had a bad connection at the connector. That motor can draw well over 20 Amps, so the connector pins need to be clean and fit together tight. I used a bronze brush to clean them and put a light coat of conductive grease on them.
Edit:
Unlike the power window switches which simply reverse polarity to the same motor winding to reverse the window motor, the convertible top switch applies 12V to one of two separate motor windings on the pump motor. One is forward and the other is reverse with the other side of both grounded. So the ground connection needs to be clean and tight as well.