Jerry, allow me to clear some things up from your post.
Good point about priming the fuel system. I have had no problems with the gear pump not self priming, but you are much better off to manually prime it. Often just filling the filters and lines with a hose, funnel and gravity is all you need. Note, because of the design of the gear pump you will not get fuel to pass through it with out it turning. You are correct in connecting the priming pump to the inlet of the secondary filter, and it would not hurt to pull the extra inlet plug from the top of the primary filter and pour fuel in it. Or, to do both at once suck fuel from the extra outlet on the primary and push it in to the inlet of the secondary, the priming pump will be in parallel with the gear pump.
The fuel system is in this order: Tank, primary filter, gear pump, secondary, inlet manifold on heads, injectors, outlet manifolds on heads, restricted fuel fitting, return to tank.
I have had the relief valve on the fuel pump stick before. It would not hurt to have a 100 psi gage after the fuel pump, it will answer many questions if the engine acts funny. It should read about 70 psi with part throttle and never much more. If the relief valve sticks closed the pressure will climb over 150 psi. If it sticks open you will have a very hard time getting fuel pressure. Without about 20 psi the engine won't run at all.
The governor will have two levers, one connected to the go peddle, and the other is the engine stop lever, probably connected to a pull to stop knob on the dash, or air cylinder as mentioned. Be sure that the stop cable is free and working.
If an injector rack sticks the stop lever on the governor will NOT STOP the engine. The emergency air shutoff on top of the blower will.
The emergency air shut off should never be used unless absolutely necessary, it is not good for the engine as it can make the blower seals leak oil. It will almost certainly draw oil by them while the engine tries to stop, with the blower drawing a serious vacuum on them. Then after that they can leak more during normal operation.
Another way to kill a runaway diesel is to use a CO2 fire extinguisher in the air inlet, this has no ill effects.
Grigg