Next should have been PCM power relay, and the associated fuses. This is hot in the run/start position and control quite a few items that deal with powering the truck.
The PCM power relay is still a serviceable item ( relay can be removed ).
The Gryphon while plugged in, is only acting as a gauge, nothing to do with the tune tune loaded on the PCM. Not much can go wrong with the truck if you use the Gryphon to monitor operational parameters.
If the dealer reflashed your PCM, they wiped out the Gryphon tune, and you basically have a digital gauge kit with the Gryphon now.
The dealer should not have done a PCM reflash, as without power to the system, they cannot do it ( unless they bench reflashed it ).
Besides the fact if they got the truck working again by changing the CJB, that should have been the end of the work, no additional labor time needed ( i.e. reflash ).
The only things I see with the Gryphon and no start issues have to do with a weak battery while reflashing the PCM, not in operational terms.
Did you ask them what was wrong with the CJB ? They should be able to tell you in plain terms, if it was that easy.
The other things that come to mind:
-Loose battery cables
-Problem with the Yellow w/ Light Green stripe wire to the CJB ( powers the buss in the CJB ). This is an easy test, with the symptoms happening, check with a meter on Fuse #10 for power on 1 of the 2 pins. If it is dead, check Connector C270P for power on pin #1, Yellow w/ Light Green wire.
- Problem with the ignition switch.
-- I know twice my 2006 has had a dead key symptom, where I turn the key, and nothing powers up. Both times when I stopped and thought WTH, the truck powered up. Not much I can diagnose when it is functioning correctly.
These items, a jump start would not fix.
Assuming you still have the same battery in the truck then ?