When you turn the D handle, the fingers of the D latch release the switch in the frame, this switch is wired to the Power Top Control Module (PTCM). When the PTCM gets this signal, it sends a command to the BOdy Control Module (BCM) to lower the windows. If the top module is not in the car, the windows will not go down.

Severe failures of the Power Top Control Module are rare, and failures of the pump are rare. Most problems are caused by the switches and sensors in the system.

The bad sound the top made when it quit working sounds like low fluid, caused by a leak. This might be due to a damaged or bad pump, but I think it was probably caused by low fluid.