Stop there.

If you turn the D handle, the switch relaxes in the frame of the windshield and the switch changes state, as long as the hook from the top is not pressing on that switch, the windows should go down all the way.

If they stop, I'd think that is an indication that the switch is indicating you have re-latched the top to the frame - so the windows stop moving.
With this indication, the PTCM will not allow the pump to start. This is expected behavior.

When you turn the "D" handle, the switch up there relaxes, telling the PTCM to tell the BCM to lower the windows. IF that is not happening, your first step is to determine why it is not happening.