Welcome! These trucks do have some problems... I would suggest having a read on the forum to see other's issues and what people are doing to help increase the lifespan of their truck.
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.