I have the same problem with my 1999.5 F350. It started with longer crank times. Then check engine light comes on during start up and takes few minutes to go out. During this time engine idles little rough. Which is few seconds. The engine surges a second or two and check engine light goes out. Truck idles ok for that period of time of use. The truck will act this way every time i restart. This is in warmer temps. Sometimes it starts right up with no hesitation. Now with cooler morning temps of 50 degrees the truck starts on the first crank. No check engine light or rough ildes. But later in the day as it gets warmer it acts up again.
Try what Kl has said first if it persists and you have a chip in remove it and try to start, see what happens then.
If all that fails get to a scanner that's capable of reading powerstrokes .
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