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I had one do that! It was so freaking stupid what the problem was...
Fuel filter was clogged. Injectors were clogged. 3 bottles of sea foam (one per full tank of diesel) and a new fuel filter later and it ran awesome. Hopefully it's something that simple for you as well. I replaced the fuel filter first, the one on top of the engine and then did the sea foam. I'd guess any injector cleaner would work fine.
I wasn't gentle with the truck either, when I put the sea foam in I took it to the bottom of the I-535 bridge in Superior, Wisconsin and stood on the throttle til it hit 55 MPH. The smoke clouds were intense, be sure there aren't any cops behind you Truck was bone stock, it was just filthy dirty.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.