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.