Hiya,
First question: Is it a true runaway where it will overspeed higher and higher until it's choked out or does it go to governed RPM and stay there? If it runs away and doesn't stop, that's fuel being introduced outside of and/or in addition to the injector and pump system, if it runs up to max RPM and stays there, the issue is in the pump and it's components and controls.
Non mechanically induced Diesel runaways are from 2 causes, either a combustible mixing with the intake air then the compression lights it off OR fuel is being introduced into the cylinders at an abnormal rate. First thing I would look at is the oil level, is it really high? If the fuel tank is higher than the pump, the pressure head over time may have forced fuel to leak out of the injector shaft seal in the timing case and fill the crankcase. Such a dilute oil would slip by the rings and introduce extra fuel in the cylinders. (long shot but an easy check)
If the oil isn't diluted with fuel, is it the proper level and the engine has proper oil pressure? I ask because some Diesels use engine oil pressure the actuate the load/governor system, without oil pressure, the limiter can't pull the fuel back and the engine races to max RPM. Next I would inspect either a fuel pin/fuel cam in the pump. (Were there kids that "played" with the tractor that could have forced the hand throttle hard while playing?) Question: In the first minute it's running, while it's still idling "normal", if you "blip" the throttle up then pull it back to idle quickly does it return to idle normally or does it slowly slow down or stay at the elevated RPM until it starts climbing? If it comes back quick to idle, the return to idle stop is most likely functioning correctly. (This is also the same test hot rodders do when "turning the screw" on mechanical pumps so they don't cause a runaway, if they turn the screw in too much, the cam/pin goes over center and the engine runs up to the limiter.)
Another thought is a malfunctioning cold start assist, some Diesels overfuel the engine slightly and/or advance pump timing on cold start to increase RPM, if this engine has such a system, if it was adding fuel to the engine, it could cause a runaway like condition.
It's tough troubleshooting without being there but hopefully these give you some areas to check.
Tom