UPDATE:
So we’ve had a decent amount of time now to go through fuses, breakers, sensors, etc. and we’ve determined that the one of the batteries isn’t charging when the engine runs. So as a result the engine is slowly draining it; causing the motor to shut down.
Any suggestions on where or what to do next? It’s not the alternator because the other batter is charging and we switched the batteries around to see if it may have been the battery (despite them both loading good) and it didn’t matter which battery was where it was the same #2 location that would not charge.