ajs:

Barring a problem with the ECU itself, the symptoms, taken all together suggest a mechanical problem rather than an electrical one. The fuel system can be viewed as composed of two components: fuel supply, and fuel metering.
The supply component includes the tank, hose to the fuel pumps, pumps, accumulator, filter, piping from filter to the fuel distributor, the pressure regulator, and the return piping.
The metering component includes the fuel distributor & air flow meter, the injection valves & lines, and the ECU & EHA.

Things are getting a bit obscure here, but an extended fuel flow test with the pump relay jumpered (10-15 mins.?) might reveal a time dependent fault in the supply. A battery charger hooked up may be required to keep the pumps running.
Have you run with the pressure regulator leak line disconnected?