Originally Posted by Diesel911

Could not hurt to change th Spin-on filter.

A small Air leak could form a bubble in the Fuel Injection Pump Housing; and when it gets big enough all or part of the bubble it could pass through your Fuel System into the Injectors.

It could also be your Fuel Injection Pump Pressure Relief/Bypass Valve is having issues. It is a Ball Bearing with a spring on it. Perhaps it does not seat well all the time.
A very long thread on the above.

Could be one of the 2 Valves in the Lift/Fuel Supply Pump are not seating well.

Somewhere in our DIY Repair section they have tests for both of the above.

Then there is the Fuel Tank. Restricted Screen (stuff could be floating around in the tank a cause issues only ounce in a while) or a restricted Tank Vent.

In this last year I have been reading of people haveing enough Crankcase Pressure due to the Blow-by that it had an effect on the Vacuum Shut off; pushing it partly in the shutoff position. At least 2 had restrected Blow-by plumbing.
I know when I blocked my Blow-by Tube with my thumb in about 7 seconds my Engine was trying to shut itself off.