Put a wrench on the flats of that "stud" and turn counter-clockwise. That's actually the shaft for the gears and the clutch discs. The "emergency closing nut" is just a plastic cap that fits over the flats. Those things are easy to break. It's obviously missing. If you can't get movement, then tighten up that big 17mm nut. It's the clutch adjustment. If you get it very tight and you still can't move the cable, then you have a bigger problem that will require some disassembly. The "rod coming from the bottom of the motor" is the take up tube for the end of the cable.

How is it that you were able to manually close the sunroof most of the way without turning that shaft?

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'79 240D