Since Bill hasn't answered you, at least here, I'm going to see if I can't make sense of this. If he PM'd you, then we'll see how good my advice is.
You first installed and made sure Pegasus was fully up to date - right?
Then, when Pegasus saw your Gryphon, it told you not to update just the firmware but instead, to "update everything" and you did that.
Now, did you notice any kind of notification of what was being updated as this process took place? I don't expect you to remember exactly what you saw, but did you see several files being written? If so, they're most likely in your Gryphon safely and there's no problem.
Now here's what I'd do and I can't see how this would hurt anything - until you actually change the tune in your truck, the Gryphon is just a monitor and cannot do any damage. Take your Gryphon to the truck, turn the ignition to ON and plug the Gryphon in to the OBDII port. You should see the truck's HEX code, and after you hit enter, you may possibly get some kind of "warning" that you have to hit enter to get past (and I may have the order of these reversed - I remember seeing both though after a Gryphon update).
In any case, keep hitting <enter> till you get to the PID display screen. If the unit has been updated I think you'll see the 4 default values: I think they are RPM, MPH, ECT and TFT (but I could be mistaken on the last two). And, you should see that you're at level 0.
If you get at least this far, you know the unit is functioning properly and I'd bet it's ok to proceed. If it doesn't let you get to this point, then Bill WILL have to help you.
Now I'd try pushing <Menu> and then Power Programming. In my case, Bill has renamed the custom tune choices. If you see choices like:
Lvl 1 - Trans. Only
Lvl 2 - Towing
Lvl 3 - Performance
then I think it's likely you have lost any custom tunes you had and again, will have to talk to Bill to get them back. (I did this, so don't worry, you won't be the first, or the last to do this). :o
But, if the tune names are different, then I'd be very confident that you are good to go and can go ahead and select any tune you'd like.
But remember, until you
actually choose a non-stock tune and tell the unit to write that tune to the PCM (by turning the key off and then back on), you HAVE NOT done anything to your truck! (And it's the expensive piece of hardware here). I really think you could probably even just unplug the Gryphon at the "turn key off then on" point to interrupt the programming and prevent damage. (This MIGHT cause the Gryphon to become unusable till reprogrammed though, however, I doubt even that would happen).
I really think the only time there could be possible problems is if you disconnect the Gryphon or interrupt the programming
as the PCM is being written. And, I bet even that is correctable.
Let us know what happens though, and if Bill has already helped you, tell us all if I was close to being right.
- Jack