I preface this with the fact that this is my first diesel. I have a '05 F350 SD Harley edition that I bought from my father-in-law. Truck has been flawless other than a small oil leak. I took it in at 99000 to have all the fluids changed and to have the oil leak fixed. Everything was done as requested - oil leak was the rear main which they replaced - but they also reprogrammed the vehicle.
When I got it back, it was sluggish compared to before taking it in, but thought that may just be my imagination. Then about 3 days after picking it up, as I was pulling up to a stop light and the engine started acting as though it lost half of its cylinders. This lasted for about 10 seconds and then it was back to normal.
On the way home, I stopped to get something to eat, and when I came back out, the truck would not start. It turned over just fine, but seemed as though it was not getting any fuel - I had 3/4 of a tank. NO Engine Light.
Truck was towed to Ford who had it a week and they could not recreate the problem. It started up as soon as it got there - they ran it hot, cold starts, drove it (used a 1/4 tank of diesel) and nothing coded or ran bad.
Got it back on Friday, drove home, it sat for about 15 minutes before we got in it to go out, and it started, but acted like it was missing, and there was absolutely no response when pressing on the fuel pedal.
Called the Ford mechanic, who indicated that it could be the FICM, Cam Sensor, Crank Sensor, etc. He said that because it was out of warranty, they did not want to just start replacing things, but it definitely acted as though it was an electrical issue.
If I let it sit for about an hour after it does this, then it will start.
This is all intermittent. Sometimes is will run just fine. Other times it acts as stated above. Very frustrating as I cannot trust it to go out as I am not sure if I am going to get home.
I also noticed that the Cruise control is not working.

Not sure if that has anything to do with anything else that is happening.
Any thoughts? I really love this truck.