From the PM I got from you I know this car is a '96. On '95 and newer models the rear latches can not be operated manually. It is safe to raise or lower the top manually. Regarding the roll bar, the only way to operate it manually is via the switch on the center console.

If power is interrupted to the soft top controller as it was in your case, then it becomes necessary to "synchronize" the power windows before operating the top. You do this by raising the windows and continuing to press the switches for 2 seconds after they are completely raised and motion stops.

Your windows are down and don't respond to the switches, so obviously you can't synchronize them. I would try reseting the system as follows: (1) disconnect the ground cable from the battery, (2) momentarily short it to the positive cable to discharge any capacitance in the system, and then (3) reconnect the ground. Once this is done, then see if you can synchronize the windows.