My 2000 ford f250 diesel truck, the service engine soon light comes on then the truck runs rough, goes off and run normal. What could this be?

See if this diesel engine troubleshooting link helps:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-8.html#post1415281

I have done all this and have had it codes tested by three different people and no codes come up.