I think we need a flow chart. I think what you are doing- for whatever reason- you are changing cabs? Lets have a breakdown of what the current set up is, and what the cab you want to swap to is.
As far as I know, all the top kicks of the same era had the same cabs, there's no difference from auto to manual, aside from the hole in the floor for the shifter, and another pedal. But if you have both cabs, none of that should be a issue. It should all swap.
The same with the brakes, the air brake will have a treadle valve, but if you have the old cab that is hydraulic brakes, it should all bolt right up to the cab.
I think you will have more issues with the wiring, if going from gasser to diesel, in swapping all that stuff over.