Wow........sorry I don't have an easy fix but I would look at the fuel lines between tank and filter and to the lift pump. On the surface, it sounds like it may be a fuel line, either fitting at tank, filter assembly or the line itself based on the way I understand your explanation.
I think if it was a lift pump or even an engine fuel pump the filter would be full and not empty when the problem crops up.
If there is any way to test the fuel line from the tank, if it was me, I would start there