I'm relatively new to the 6.0 PSD, after having a 12v 5.9 Cummins in a Dodge for 10 years, but the only quirk I've noticed is directly related to the drive by wire setup. With the traditional linkage on my Dodge I could pat the throttle to get a quick snap of power when I needed it. With the drive by wire setup the computer prevents a quick snap to the throttle. After having Ford fix some rather minor (but annoying) oil leaks I've been pleasantly surprised with my 6.0 PSD. I thought it would be a dog after so many years of using a 5.9 Cummins on steroids, but it has performed extremely well; much, much better than the '99 7.3 PSD I had. Even with a chip in the 7.3 PSD the completely stock 6.0 PSD has way more power.
I'd look at what the other guys familiar with the 6.0 PSD said and possibly even the drive by wire system. Before I bought this truck earlier this year I looked at the new Dodges and the newer Duramax pickups. I felt the front end on the 4X4 was light years ahead on durability when compared to the GM offerings and had overall far better axles and suspension systems. Maybe I'm old school, but with the Fords and Dodges offering the traditional solid axles and proven heavy Dana axles front and rear I felt far more comfortable. Of the two, the Dodge and Ford, that made it to my final cut, I rather strongly preferred the ride, drive, styling, and interior quality of the Ford better this time. With the wide variety of early problems with the 6.0 PSD I did hedge my bet some by buying Ford's 7 year and 200k mile warranty on the truck for a little over a grand. From speaking with GM, Dodge and Ford dealers, I found that Ford was the only manufacturer to offer a 7 year 200k mile warranty on their diesel pickups.
It sounds like something relatively minor from your description but I know nothing is minor if your truck isn't running. Good luck!