If you unplug the level sensor from the harness, back at the pump relay, the system will think the tanks are full. This will tell you if it's an issue with the level probe.

If the level probe just bounces low for a few seconds, it will only illuminate the yellow light on the gauge but not turn it off. If the level probe is low for twenty seconds continuous, it will turn the system off and a key(IGN) cycyle will need to be done to reset the system and get it to come back on.

It sounds like an intermittent power source to the controller. The red wire to the injector sense wire, the red on the gray cable. You should check your grounds as well, as if these are not good you can also have issues.

Try the level probe first, but the symptoms sound power/ground related.