Mike,
1) If everything else is OK on your Mag 20, then a Gov. gear gasket kit and 2 evenings will have it back in the game.
2) Adding a Kubota to a 982 is a HUGE undertaking. You will need donor engine cradle along with radiator, etc., new fuel tank, new wiring, battery tray, new throttle cable, key switch, (actually most of the dash accessories are different). Possibly drive shaft. Without a diesel donor tractor you would be spending a lot of time finding individual parts. Diesel swaps are more like frame swaps....you swap the frame out from under the diesel components. Easier to just find a diesel and sell your roller 982....
I'd try to replace the gov gear in the Mag......not out anything to tear it down, especially if it is still running as it should, just with no gov. control. I've been into several and they are easy enough to work on.....
BEST outcome is probably a Command swap out of a 2000 series Cub.......that is basically bolt on....just need to find a donor 2000 series.