1999 Detroit 12.7 Misfiring.

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Both the timing sensors do not have pigtails on them the harness plugs directly onto the sensors. Because of vibration the connectors on the ends that plug into the sensors can wear and loose their grip on the pin in the sensor.
I have seen two engines that had intermittent misfiring that were fixed by replacing the sensors and the Metripack connectors and plastic connector bodies.

 

To add to this, we had one truck that would run for a day or two and then super hard to start and when it was running, ran so rough you could see it shaking from 200 feet away.

it turned out to be a combination of a sensor problem and the wiring harness at the sensor end. We replaced both the timing reference sensor and synchronous reference sensor, and had the ends fixed.