I have a 3 cylinder Kubota BX23S Diesel that starts to malfunction and misfire after it has been running, warming up and bouncing around a bit.
Check for restrictions and leaks between the tank and the pump causing a lack of fuel supply. Install a clear hose in line and look for air bubbles in the system and check that the fuel supply pressure is constant. If so, it points to an injection pump or injector problem.