Ford 6.7L Power Stroke Diesel :: 2013 F350 - Shuddering At 50 - 60mph

My truck shudders bad between 50 and 60 mph. I have about 7,000 miles on my 2013 F350 diesel. 4x4, single rear wheel automatic. My truck has had this issue since I drove it off the lot. I replaced the tires and wheels with after market 20 inch wheels and toyo mud terrain tires, added a leveling kit and installed a K&N intake at 2000 miles. When driving between 50 and 60 mph with a steady pedal my truck begins to shudder. You can hear the noise coming from the intake, which is not the problem. The boost is registering almost no boost what so ever. The problem mainly occurs in 6th gear with no load or a light load. The entire trucks shakes.

Since I put more miles on my truck each day the problem seems to be getting worse. Not to mention my mpg has drop since I first got the truck from 18-20 to an astonishing 14-15. I took it to the dealer the other day to let them figure it out. They put stock wheels,tires,intake back on the truck for testing. They determined that the shuddering happens between 1400-1700 rpms. They told me they couldn't find anything wrong with the truck and said it was my wheels. They mentioned that with the stock stuff on it was less noticeable. They also said that with stock wheels and tires it went away. Which I know is crap cause I had stock on the truck for 2,000 miles if not more. Now this is a given for anyone who puts mud terrain or all terrain tires on their truck, MPG will suffer some and there will be noise and vibration. However, this is more than a vibration from tires. I have only owned trucks all my life with bigger tires and wheels on them.

I walked out of the dealership having to pay them money because they said it was due to my wheels. My wheels are 0.4 inches off from stock and my tires are the exact same height as stock just wider. Knowing a decent amount of mechanics and how to put my pants on each morning, I was not satisfied with their conclusion. I mentioned if it was my wheels and tires why wouldn't it do it all the time. It's not like I replace my wheels when I'm driving down the road. I believe that they couldn't figure it out so they said it was my wheels and tires to charge me for the time. Just yesterday I was driving on a long trip and it was shuddering, then the cleaning exhaust filter notification came on and the shuddering stopped. I noticed this and tried to make it shudder, couldn't do it. This reinforced my theory that the dealership is less than knowledgeable.