Welcome! Congrats on the truck. As far as your wheel hubs, I'll let someone else chime in on that. I've only had to replace one my whole life and it was just wore out!
It sounds like the truck isn't regenerating properly. Did the dealer do a manual regen to help clean out the filter? If they aren't helping, I would find another dealer.
Winter starts are fine with the EcoDiesel.. as far as fuel mileage.. lots of variables here but a 65-75% highway trip should net 25+ MPG pretty easily.
Welcome to the forum! I would advise to drive it and see how you like it. The EcoDiesel is great on fuel mileage and if you don't tow very heavy, it's a great truck.
"Stacking" tuners really isn't needed anymore and is old school.. GDE (or any custom tune for that matter) can get just as much out of the truck as two devices put together.
There's a transmission harness with a connector up beside the trans itself, check it and be sure it's not loose. I've heard of many weird issues if it's wet or doesn't have a good connection.