some people call the supply pump the "injector pump".
I doubt it's an injector issue. Usually on these if there is a problem, generally they bypass and it either is very hard to start or won't start at all, and have codes for low rail pressure and sometimes high rail pressure. But again you need the software and hardware to see that stuff. IOW, dealer only at this point.
Explain runaway. Generally when I hear runaway in the same sentence as diesel engine, one of two things are the usual cause. (A)-the fuel system is malfunctioning such that it cannot control rpm with fueling. Since there is no throttle valve, there is nothing else to control the engine speed. Or, (B)-it's running on it's own lube oil. On L3301/3901 and others, this was an issue and there was a recall for it, but only on the very early models (like 2013/14 if I remember right). Basically Kubota put a tiny plug in the valve cover crankcase vavle vent when they painted the engines. On a few of them they forgot to take the plug out, and they'd stick-allowing oil to enter the engine's intake manifold. Diesels will run on their own oil. An oil level that is grossly high can also be a cause, so you might look at that. So your description doesn't really compute in my pea brain. maybe I'm misunderstanding? And how do ya know there's nothing in the cylinders? Have you had it apart or??
but with the codes you've talked about, I'd expect a can system error, perhaps something that reads the control side of the crankshaft speed position sensor. That sensor is located behind the RH side loader main frame kinda in front of where your right foot goes. Sensor is buried back in there, reads off of the flywheel. There are (I think) 91 holes in the flywheel that it reads off of. If the sensor or the can system has an issue it can't properly read the crank position (or speed) and thus it will begin to lose control over what is happening. Generally you'd see a crank sensor code populate, along with an erratic RPM reading in the digital tach (which is part of "A" mode in the panel).