The PCM supplies a "clean" ground for the sensors. That is, the sensor grounds run back to the PCM itself, not to the PDC. The PCM gets it grounds from the harness grounding to the engine. This ground is usually at the front of the engine, between the water pump and power steering pump. This means the engine itself needs a really good solid connection to the negative post of the battery.
So, since you have a trunk mounted battery, did you ground the battery to the body or is there a negative cable running from the battery all the way to the engine itself?
Is it setting any trouble codes (DTC)? Do you have a data link connector wired in to check for DTCs? Is it losing fuel pressure when this happens before it actually stops running? What do you have for a fuel pump and where/how is the fuel pump grounded?