I've got a 08 F-250 with the 6.4. A couple of weeks ago it started to hesitate real bad and the check engine light came on. I changed the fuel filters and found
alot of trash in the low pressure pump. I cleaned it out and got it flowing through the water separater valve again. I've drained it several times since then and drove the truck to work and back (about 15 miles). Today the hesistation was even worse ( a trip over 30 miles one way). At some points it seemed to run fine and at others it would hardly pull. Autozone said the code was bad fuel rail pressure sensor. The three causes they gave me was bad sensor, bad connection, and clogged fuel filters. Do the filters need changed again or have I messed something up. When I changed them I got sand, wax, and grass out. Should I drop the tank and clean it also.

 

Moved to the 6.4L Powerstroke Diesel forum.

 

there are a number of frp codes to choose from, knowing the exact cood will help you on the path to correction.
my guess is a p0088 there is a reflash for it but if the pump is bad it wont fix the concern but its a good first attempt

 

I think in addition you should take the cover off the fuel water separator and clean it again. And new filters...I assume or would hope that you used only the motorcraft filters.

When you take the top mounted one on the engine out shine a light in there and see if it is completely clean. No rust or debris.