Does your truck have an EGR valve on the intake?
If so, try disconnecting the vacuum supply and see how it runs. Then try to give the EGR valve shaft a good flick with a screwdriver to help it seat. Also you could just remove it and check to see if the valve is seating.

I'd be very skeptical that it is anything to do with the computor....like has been mentioned it's more likely to be a sensor/injector/egr problem.
I've seen ton's of trucks come in with stuck EGR's or bad EGR transducers (the black vacuum pot on the EGR).
Please let us know what you do find.