Not sure why they can't regen with the dealer tool.. if the sensor is bad, I'm guessing it'll likely fill back up to 100% full again and that's why they didn't do it the first time.
The "Dead Pedal" after the software fix is really bad. I wouldn't say all diesels are like that, it just isn't true. I would recommend selling the truck or tuning it if you want the throttle fixed.
Looks great, the wildpeaks are good tires in my opinion! I have a set with about 40K on them and they still have a bit of tread left. I think one could get 50k easily on them, maybe even 60k.