It's easier to start with an organ that's only one part and has mod wheel opposite of what you want.
Much of this general navigation is covered here:
https://www.yamahasynth.com/modx-category/mastering-modx-navigation-tips
Recall one of those Performances.
Use the touchscreen to touch the PART (only part there) from the [PERFORMANCE] (aka HOME) screen. It's one of those vertical rectangles under the Performance name.
A menu will pop up - choose "Edit".
"Common" (lower left) should be selected by default. Touch the touchscreen (left hand side) "Mod/Control" -> "Control Assign".
In the upper-left there should be a button "Auto Select" - make sure it's green.
Now move the Mod Wheel. The parameters assigned to Mod Wheel should show up automatically after moving. You should see a rotor speed. If that is not the selected destination, press it to select. You're going to want to reverse the curve so the parameter is changed in the opposite direction. You could use user curves to draw a curve that is opposite what you see on the screen - or pick a preset curve that will mimic this. What this does is still adds to the default programmed value - but reverses the direction. All the way down will be adding maximum and all the way up (rotation of MW) will add the minimum.
You could also change the polarity of the curve that is presented (usually it's a positive ramp) to a negative one. You'd also have to go and adjust the default programmed value for the rotor speed and increase the value. If the curve was positive, the default is likely 0. When you switch to negative, you should set the default to 127 (or some high value). Since now you are subtracting instead of adding to the number.
I can put something more specific (an actual organ and running through) once I get the keyboard setup. Unless someone else beats me to it. That's the general rundown.