Appreciate the replies and thought I'd give an update.
The trim codes ended up being the easiest part of this disaster, had some time last weekend so I pulled the valve cover and used my phone with a small work light to take pictures of each injector and got the codes which was relatively easy. Sure enough, all the ones stored in my ecm after the last crash were bogus and didn't match the ones on the injectors.
My ecm is still out for "refurbishing" with no word back yet. I'm starting to get worried I chose poorly in where I sent it and also for not trying another recovery flash with freshly charged batteries. I guess time will tell.
TCDiesel, when the truck was disabled I tried looking at module information with a scan tool and the ecm would not communicate so no ability to write the vin to it. The only way I could find to revive it is to flash it with a recovery file provided by the tuner company which takes it back to stock and I believe is somewhat similar to what a dealer would do in flashing the ecm but not sure. The scary mystery is why the ecm becomes corrupted.