Loss of power

[toad]

I am working on a 2004 6.0, 34,000 miles, and a six speed manual. The truck runs fine until you shift into overdrive then it completly bogs down until you get up to about 2300 rpms it does not do it in the other gears. It feels like a misfire. The fuel filter has been in for 5000 miles. (yet it has sat for almost a year) while the guy was deployed.