Misfiring, low boost, no power???

[Gump1986]

I have an early 99 F350. I converted the truck from an auto to a manual transmission in January, along with a Southbend clutch, Beans chip, and Stage 1 injectors. I also replaced the o-rings, glowplugs, undervalve cover harnesses, and valve cover gaskets.

Two weeks ago the truck died headed to work. I work out of town, and only place doing diesel was a Ford dealer. Had the truck for 2 weeks, they did the CPS and fuel system integrity recalls, and said the IDM was bad. Installed a modified IDM from Beans...

Picked up the truck, it ran ok for a day, then started missing and running rough again. The truck misfires, idles rough, runs rough, and builds little boost. A compression and leakdown test came back normal, ICP pressures are normal, and fuel pressure is normal...Buzz test came back fine, Contribution test shows #3 and #8 are gone, and #7 is failing...

There aren't many parts left on this truck that I haven't replaced...anyone offer some help? I'm stumped...