What could be causing this sputter?

Is there a shut off valve near the filter? I’ve never had a problem, just pre fill filter. Even if I don’t shut off the valve, and change it quick. The hand primers a pita. They always leak, break, only needed when ran out of fuel, or maybe when you changed fuel line.

 

They say not to fill filters because few people know or care enough how to do it right. (Fill from sides not center hole is correct)

That said, when truck was operating correctly, (ive got same engine) even without using primer or ether my truck would start right up no problem after a filter change with them put on dry.

Consider looking for bubbles on your suction line
(kwcam had a good culprit to look for, i replaced all suction lines on a truck before i found that one after i replaced the hvac control on a w900)

Lazy way to find a suction side leak is to lightly pressurise your tank (like 5 psi) then go along and look for where you have fuel coming out of a hose or fitting

 

I had a 3406C. Not an E. I always pre filled them. Same now with my 12.7. They’re worried about bad fuel. Dirty fuel, water whatever. Fuel pumps have filters. I’ve never had a problem. The fuel gets water usually from condensation in the Truck tank. Lot of Guys used to fill them with transmission fluid.

 

I got rid of the primer pump on my mxs because they are so restrictive , i pre fill my filters , the exact same ones the OP uses and i never use either . Definitely sounds like sucking air . My brother had weird problem like this and we found the plastic coating from a soda bottle inside the tank . Every so often it would find its way to the suction line and cover it over and shut it off . you didnt happen to use a soda bottle to get fuel out of the tank ???