Is your crank signal wire anywhere near spark plug wires, coils, injector wiring, etc? You mentioned above the harness is pulling on the sensor. Did you remediate that? Perhaps the connector has been damaged from being pulled on? Is the crank sensor a VR or a Hall sensor? I'm not as familiar with Holley as I am with MS, but a crank signal will be all kind of wacky without a pullup resistor and the MS will see a signal like this.
