I have seen some models and flashfiles have injection disabled but not tell you what the problem is in ET. Some dozens have a 3 pin connector that you flip end for engine to disable injection. This is found on the main engine harness sometimes. Some remote shutdowns also will not tell you in ET. They are usually NC (Normally Closed) circuits. If you say there is no remote shutdown in your system the harness may need to have a bypass added.
Finding the remote shutdown pin on the Schematic either at the ECM or the customer connector plug then wiring it to ground should work.
You also mentioned the ship side of the wiring disabling the injection which could be a shutdown somewhere or a bypass missing.