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When you ran 12V directly to the pump, did you also run a separate ground?
Have you checked the ground wire to make sure it is not broken?
Yes, I ran a separate ground from the battery. I checked what I could on the ground wire, it appears to be ok. I am guessing that if I placed the volt meter on the positive terminal of the battery and the ground wire from the control box this would check the integrity of the ground?
Also, with the fuel pump connected to the control box, I pushed the prime button and measured 12.5v across the pump. Without the pump attached I was measure 13.5v across the wires from the control box.
To check the ground wire, you will need to disconnect the fuel pump, and use an ohmmeter or continuity checker to test from the wire to ground.