Fuel supply issue
This sounds like a fuel supply issue. There is enough fuel in the system to run the engine for a short period of time, at which point the engine struggles for a fuel supply. I guess it is remotely possible that your previously overheating engine fouled the fuel injectors. My best guess though is the fuel filter body on the top left side of the engine. There is a seconday filter in there. It could be fouled or the bleed screw on the top could be leaking air into the fuel lines. Regardless I would make sure that the fuel system is bled out properly. In the past I have hand filled the fuel filter body assembly on the engine, not the primary Racor filter, and run the engine. If it runs fine until the fuel is gone then you can probably eliminate the fuel pump this seconday filter. I do the same thing again at the primary, Racor, filter assembly. If it is still fine then I would suspect your pick-up line in the fuel tank itself. Do you use an anti-growth additive in you diesel fuel?I would also check the engine linkage cables. Go down below and have someone start the engine in neutral. Run it up to speed while you watch the cable at the engine (Just above the transmission in the back of the engine). You may find it is slipping there.Follow the entire fuel line. You may find a kink or a pinched section.BTW. When I had my cooling core replaced for the same overheating problem on my 3YM30 the positive wire to my alternator was not attached securely. The alternator had to be removed to access the core. It arced and sparked until it burnt out and no longer was charging my batteries.Good luckAndy