Help. 6.7 won't start
 

So this is a brain teaser. Need some out side help. Truck has full deletes and has h&s XRT pro. Guy had injector #2 swapped and truck has had troubles since. Dealer replaced injection pump and fuel is getting to injectors. Truck tries to start with just a sputter then quits. Will keep cranking but won't try to run at all. Unless you cycle key. I returned ECM to stock searching for codes and none popping other than the norm for deletes. Tried flashing ECM and result is same. Need ideas. Truck also has auto start but owner says its disabled.