This sounds like an electrical or computer problem. Zero boost for a period of time and then regaining the boost necessary to travel at speed doesn't sound like a hole in the turbo charged air system. It doesn't sound like a fuel filter either. If the fuel filter were plugged, it would remain plugged.
If your Cummin's is like mine and it sounds like it is, the primary fuel filter could be working intermittently. Even when it quits working the secondary will suck fuel through it but not at a rate necessary to run at speed.
Like other, I think your going to have to resort to having someone pull codes.