The R129 is more complicated than down / up.

Later cars ( At least from 97 + ) drop the windows a bit when you pull on the handle. This is because the glass under the upper weather strip for better sealing. Early cars ( 90 to ? ) might not drop the glass because it rests against the weather strip.

The windows are tied into the top controller so they lower when the top is being moved.

Later cars can raise / lower the windows by pressing and holding the remote lock button or inserting the key in the door , turning to lock or unlock and holding it until the windoes complete a cycle.

You need a wiring diagram for the year / version you are working on as there are several versions. You might be able to send a signal to the window controller to make things move.