If you want the expression pedal to work as intended - to control the expression - you should go to the concert level and adjust these features in the Layout mode. The Screen Control Inspector should look like the image below. Make sure to change the Number dropdown to #11 Expression:
If you would like the expression pedal to control the organ rotator speed, you will have to do a few extra steps. The rotor speed only has 3 positions - slow, fast and off. You can map any toggle or button MIDI control to this function, or you can use the expression pedal if you would like. By using the pedal, the rotor will switch to fast when the pedal is halfway or above, and back to slow at halfway and below. To use the expression pedal he will haveto go back to Layout mode, and change the Number dropdown menu to 18 (General #3). Then connect that via the Vintage Organ instrument plugin. The Screen Control Inspector should look like this:
In the Vintage Organ Instrument plugin, you will need to go to the Rotor Cabinet screen and change the Speed MIDI Control to "CC #18 Temp." This will connect the expression pedal and the rotor control within the instrument. The plugin should look like this:
This will allow for the expression pedal to toggle between the slow and fast speeds of the rotor, which can be further adjusted by using the knobs in the Motor section of the plugin. If you would like to assign another button or toggle control, you will have to select that control in Layout mode, assign it to #18 just like you did with the expression pedal, and follow the same steps in the instrument plugin.