You need to have your codes read, this will tell you what the problem is. Then you need to get a lawyer and sue that dealer for taking you to the cleaners. I am so glad I have neevr had to take my truck anywhere near a stealership.
Since you are new let me also tell you to get that K&N filter out of your truck quick!! They have been known to dust many PSD'S. It is so bad many dealers will cancel your warranty if they even see one. They don't seal right and they let way to much dirt into the engine and dirt is death to a diesel. I hope you haven't had it in there long or driven in a lot of dusty enviorments. It takes months to dust a motor, but it does happen. If worried pull your intake and shine a flashlight at the turbo blade, if it has small chips or rolled edges it means you have enhaled dirt, also look for dirt on the inside of the intake tubes, there should be a slight oil film, but no dirt. You can get rid of the oil by doing a CCV mod ( PM me for more info on that), if you want the best filtration possible get a Ford AIS intake ($200 from powerstrokeshop.com) or you can do a SrageII it will flow a bit more air, but nothing filters better than the AIS. The element was designed for use in the Humvees during desert storm to keep them running.
Good Luck