How low is the air? Is the buzzer going off? Are the air gauges showing less than 60 psi?
You can get a little plastic air valve from Home Depot or similar to close that line. I have several places I've done that while I'm building my bus. I got mine at Runnings for like $7 each.
Here's an example:
I'm not sure all of the ways the md3060 communicates with everything, but low air pressure *might* prevent the system from letting you put it in a gear. If you can't get the air up to 90psi on the 2 gauges, then I'd go cap that line.
After that, if it still won't shift, there are ways to get the transmission to show codes on that shift module to make sure it's actually communicating. I'll have to look up how that's done.
Again, first thing is charging the air system. I'll dig through my electrical diagrams and see if the low air pressure circuit does anything more than make the buzzer and light go off.