The Powerstroke engines are only sort of OBD-II compliant. A standard code reader won't work for anything other than a few generic codes. Some of the aftermarket programmers will read the ford unique codes, there's the Autoenginuity software for a bunch of money, or a professional scanner for even more money.
Agree what you're describing is most likely the cam position sensor. They're known to be flakey, mine left me stranded a year ago. Stalled, would start back up, run for a few minutes, then stall again. At that time they were $150 plus, now even the ones at the Ford stealers are in the $25 range.
Its located on the passenger side of the engine near the front - you have to reach it from underneath. It's held in with a 10 mm bolt & a clamp. Takes about 10 minutes to change.
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