When you hot wired the pump, did you disconnect the old wiring, or just connect in parallel to the old wiring? If you just hot wire the pump, leaving the original wiring in place, then you may have also been supplying power to the ECM backwards through the fuel pump wiring. Somewhere up front is not getting power to the ECM and since the ECM turns the fuel pump on and off, if the ECM does not have power, the fuel pump will not have power. If you hot wire the pump, it will effectively hot wire the ECM.
