Magnum swap starts, does not run

So it starts and runs for a few moments , then shuts down. I'm not too up to speed on your particular set up. That said, there should be a crank sensor at the flywheel housing, I would check and verify it's generating a pulse to the control unit. I believe that is what is used for establishing #1TDC . If it can't establish #1 , it might not be able to tell which injector to "fire" and for how long. Just something to ponder.