I know little about DURAMAX but I do know diesels. It sounds like it's getting on air somewhere. One or more injectors could be bleeding down causing it to shut down. This could also explain why it won't start at times. If an injector is leaking when the truck is turned off them then it's pour raw fuel onto the cylinder which could eventually wash out that hole. You def want to fix it before that happens as that will def cost some decent money to fix. Also the crankshaft position sensor should cause a check engine light to cone on if something is wrong with it. Mines an 02 5.3 gas burner and I had a check engine light cone on. Scanned it and found it was that same sensor. One final thing I have seen. Those fuel filter housing can get stopped up themselves. Not sure what you did to rebuild it but did you replace the plumbing in it? I have replaced lots of them on other brands because they had 15-25in/lbs of restriction in the housing itself cutting fuel pressure off. However I would think that if that were the case the problem would be more consistent rather than sometimes. I have also see many times some foreign object down in the fuel tank that you can see just looking down in the tank. The rubber peice that sits inside a coke bottle cap that was ever so often sucked over to the pickup tube and causing it to go dead. We worked on it 5 days before finding our smoking gun. That is a very hard problem to find. Have you tried running it out of a bucket when it wouldn't crank? If you haven't then try that next time. If it cranks right up then that may isolate your problems from being behind the pump to in front of it. Good luck man...

If your decoy doesnt have holes in it, your not letting him get close enough... J.H.

"Life lessons are almost never found where you think they should be, sometimes they're in the middle of a small, muddy creek in the woods with steep banks"... DeadorAlive