I very much doubt it's the module. If the roof stopped half way it's because it thinks the windows are still up. As Lea says, there are limit switches in the doors for this as well as Hall Effect sensors in the motors. Operate the roof by hand so that it's stored. Make sure the windows are up fully and the doors closed. Pull the fuses 4 & 5 in the boot with the ignition off and replace. You should hear the windows resync. If not then reset the windows and roll bar as mentioned in the manual and do it again. If the windows operate with their one-touch function it means they are correctly synchronised and the Hall Effect sensors are working.

The roof should operate providing it doesn't think it's closed (i.e the rear latches shut but the front open. If it doesn't work then lock the front of the roof by hand and let the rear portion hang above the latches and push forward on the soft top button to lock the roof - the windows will need to be down for this obviously.

You should clear all of the codes as a matter of course.