There are two sensors that control fueling rate: manifold pressure (MAP) and throttle position (APPS). You've eliminated the APPS by having the issue with cruise engaged, so you're left with the MAP. It can fail, but still remain in its expected voltage range (what the ECM considers normal) and not throw a code. Possible, but not probable, due to how abrupt the fueling cuts out and returns. A sticky sensor would probably be slow to react or not react, not cut out and in. Bad wiring would probably set a code.
The other sensors that control the engine fueling are the IAT (intake air temp) and the CPS (cam/crank position sensor). Most likely the engine wouldn't drop out due to a bad IAT (especially without setting a code). It is just there to advance and retard the timing based on charge air temperature. The CPS times the injection events to the appropriate cylinders. That will cause the engine to cut out if it fails, but a code is likely. The CPS also runs the tach, so watch for the tach to fall to zero as the truck stumbles with a bad CPS.
That's it for inputs. All that info goes to the ECM. Potentially you could have a bad circuit there, but not likely. Again, you'd probably see codes or have a funny wait-to-start light.
And the ECM has a direct path to the VP44's computer with some nice, big, secure, watertight connectors (might be worth carefully unplugging and inspecting). The VP44's computer does some error checking as far as the electronic inputs and outputs, but it has no idea what is actually taking place mechanically inside the pump or what the quality or quantity of the fuel shot is.
Something else to check would be the ground strap from the engine to the battery. Grounding issues can cause weird things electrically. However, you'd probably see some codes pop up, such as improper voltage at some of the sensors. If you live in a road salt environment, the front driveshaft on a 4x4 will throw salt water all over the left side of the engine all the way up to the hood, so just checking all the connectors in this area wouldn't hurt.
You have adequate fuel supply, so that's out. A leak in the fuel system would probably show up with some hard to start issues or a wet spot, so that's not likely either.
With all that being said, as someone who had a reman'd VP44 last less than 50k miles, I think your VP44 is on its way out. As diesel4life indicated, there's a wide range of what passes for a "rebuilt" pump. There was a visible difference between my #2 and #3 VP44, with the #3 (from Schied) looking much cleaner and more neatly put together on the outside. I'm only speculating that the outside appearance reflected the inside craftsmanship, but I'd like to think it was an overall reflection of pride-of-product. Like I've said, they've all broken at least once at this point. Now it all depends on the quality of the rebuild.
Good luck, and I hope I'm wrong.
Attention: TDR Forum Junkies 
