So no one got hurt and that's the important part.
Clarifying what
@Will L. said: Only pinch the return line if the engine is at idle. During run away the engine cooling fan can fail flinging blades off. Flung metal fan blades are like a lawnmower blade and can go clean through you. The hood normally contains this type of fan failure: Leave it down. Engine failure from Diesel run-away, well, the safest place is in front or behind the engine.
FWIW: what you did was disconnect the batteries and the alternator electrical noise went nuts. After the engine starts the batteries are a 2+ AMP
DRAIN on the system. Batteries also stabilize the voltage and filter out alternator noise. The alternator is powering everything when the engine is running. So with crazy voltages and "noise" the ECM and PMD lost their mind. I am guessing biased on loosing positive battery post connections off-road and electronic things getting weird. (2009 year... Radio went nuts door and locks unlocking and locking.) Normally a run away is
Condemn and replace the PMD as some are known to run away.
"Pulled F/SOL fuse, it died" ... Yea that fuse pull dropped the Fuel Shut off Solenoid (Or cut power to the PMD). It's the tall silver barrel on injection pump with 2 wires on it. It shuts off fuel to the IP when it looses power. This just cuts the fuel with key off. There is no ECM programming to do anything with it during a run-away event.
You were thinking of a rebuild: is the run-away why? I am not asking about "restore a classic." as that is different than rebuild/replace an engine.
However is it using any coolant?
Take the oil fill cap off and then start the engine: any blowby out the oil fill?
The GM manual starts with
AIR in Fuel. X2 to start there with the clear line, check fuel lift pump in frame rail works, etc.
You just got this... Changed Air filter? Fuel Filter? Old fuel in the tank? Aka Did it sit a long time?
If it's cold out and ideling a long time it's possible to cool it off enough that the fire goes out in a cylinder. Low compression and other factors help. Summer fuel gelling in a cold winter?