You may also have water or diesel bug in the fuel. Water will plug up the pores in the filter. You can put in an additive for both water and diesel bug. I had diesel bug a couple years ago and finally ended up pumping out the tank to get rid of it.

What size primary and secondary filter element do you have? The filter on the 2GM just before the high pressure fuel pump is 2 microns. You should use a 10 micron filter before the fuel lift pump. I've got a Racor filter that has a manual pump on the top of it. When the filter starts to get plugged, you can hear the RPM drop and increase when manually pumping to pressurize the fuel system. You also might have a fuel lift pump (located on stbd side of engine) that is going bad. This has the handle on it so you can manually prime the system, but I've never been able to get that working effectively. I use the pump on the Racor to prime and bleed the system.