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key on, off, on, off, on. look at the odometer window, it will throw codes at you
I would look for a p0121,p0122. APPS issue.
Also check low side fuel pressure, no less than 10 at idle.
either of these could cause the problem. If you see a p0216 code, that is a timing issue inherent to the VP44 pump. It can be caused by low inlet pressure, so don't worry too greatly.
If you see p1688 or 1689, be prepared for a new VP pump in the near future.
Other thing is, if he's running a chip. Disconnect the chip completely, and see if the problem goes away. I have seen many problems with the VP44 trucks rectified, by simply removing a glitchy performance box.