FYI - I just thought I would post this. This started recently and immediately. I would start the ol' girl (6.9) and and she'd run for a minute or two and stall. During the run time she sounded as if there was air in the fuel, not smooth and a bit rough and light. I began to think it was my pick up tubes in the tank but it was occurring on both tanks, even when full, so I decided to check my water separator first. I removed the separator from the circuit and put a clear filter in its place where I could monitor fuel supply and quality during this time.
The water separator was indeed the problem as it was letting air into the fuel line. I got the present separator from a fellow member years ago and it was a crap-shoot on how long it would last, but I cleaned it up and replaced some seals before installing it. Anyway, I'm going to put a new separator in the circuit, but they are discontinued.