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2006 F350 6.0 PSD totally stock. I pulled into the gas station this morning and it started to run rough. Never happened before. There was no check engine light and nothing coming out of the exhaust. I shut it down and fueled up. Started it back up and it was still running rough as if it were going to stall. I pulled out from the gas station and it kept doing it. I gave it some WOT for a little bit and it stopped. Drove another 60 miles and all seems fine. I have 125,000 miles. During all of this I couldn't see any white smoke coming from the exhaust and the temp stayed normal. Is my EGR cooler going out? Should I be worried? Any advice is helpful thanks.
The low fuel light had just turned on, but that has never happened before. Do you think that's what could have caused it? Maybe some dirt at the bottom of the fuel tank?
It kinda sounds like you sucked some air into your fuel system. If it's running fine now, I wouldn't worry about it too much. Best to not let it get below 1/4 tank, air is VERY hard on these injectors.
Yes, that's what I try to do. I have seen my fuel light a few times though with no issues. Also, with the 6.0L it's very important to change both fuel filters regularly (every 10-15k) and drain your fuel/water separator on a regular basis. If you can keep your fuel system healthy you'll eliminate a lot of common problems with the 6.0L.
How do I prevent sucking air? Stay above 1/4 tank?
Yup stay above 1/4 tank when possible. There is a little bright orange rubber valve or bypass about 2" up on the boot at the bottom of the fuel suction tube. Sometimes it will fall out or allow air to bypass which can lead to your truck shutting down or running rough around 1/4 tank due to air in the lines or starving for fuel.
On the left frame rail next to the transfer case. That is where the primary fuel filter is too. If you haven't changed filters at all, do it ASAP and ONLY use Motorcraft or Racor filters (Racor makes them for Motorcraft).