I'm no expert - but I'm pretty sure you should be able to get diesel out of the bleed on the filter while it's running. That you don't, suggests that there's a problem with the lift pump. The lift pump has to be running as long as the engine is, assuming the tank is below the injector pump.
Is it an electric lift pump, or is it mechanically actuated? If the former, I'd suspect either the wiring/switch, or maybe the motor itself. If it's mechanical, then suspect any linkage, or maybe it's broken internally. That you can manually lift fuel does at least give you options; worst case scenario, rig a gravity tank above the lift pump, and fill that manually, then let the engine run from it.