10,000 is a about the max life of these fuel filters. I can really tell at 12,000 that it is needed changed at WOT so I ususally just change around 7500 miles when doing all other routine maintance. If the Banks can read data off the OBDII port like the desired fuel rail pressure and actual fuel rail pressure you could tell if the fuel rail is running dry. I would say that is your problem but like you mention maybe the Banks. Banks alters codes between the ECM and engine so hard to say. Just need a device like and Edge Insight, MSD Dashhawk II, or EFILive Flashscan V2 to monitor those PIDs. I leave defuel in if running a non built allison. Trans-go may help but not a built transmission.
Brian