Make sure you are getting fuel "to" the injection pump.
you must make certain the fuel is getting TO the injection pump....
you mentioned you replaced the secondary filter a second time... how about the primary?
primary filters usually need changing more often than secondary does...that is if you are using good primary filters.
the secondary is only an insurance filter to save the pump in the event of a primary filter failure. the primary should do almost all of the work.
if you had any water in the lines or maybe a bit of residual in the tank, it could have clogged the primary....
almost always there is a balance point in the life of a fuel filter where the engine will continue to run with a dirty filter because the lift pump is pumping faster with a bit more pressure than it would be when its cranking.
so, when the engine gets shut down and then sets for awhile it will not be able to create the pressure or the volume to supply the injection pump for start up....
on the inlet sideand the injection pump will NOT help suck the fuel. an injection pump in good condition needs at the very least 8psi to allow it to create the pressure the nozzles need to pop and spray the fuel...a worn pump may need a few more psi to operate well enough to get it going.
a good lift pump will deliver between 18 and 22lbs of pressure, and if it doesnt deliver this pressure its because it has some wear in it, although it may continue to deliver satifactory service for a few more years, but if the output pressure is down below 15psi, its time to replace it.
as for the injection pump going bad, it would be a rare thing for it to go bad all at once....especially where you had it running fine just a bit earlier..
usually injection pumps fail as they set, over time, with contaminated fuel in them.... internal rust/corrosion.... then the internal parts cant move, or they do move and then stick....
UNLESS there was a bad filter that let some contaminants thru, but as unlikely as this is i think you will find the problem elsewhere.
make sure the fuel didnt all run back to the tank in the supply line.... ive seen where this has happened and air had gotton into the line... then when the filters were being primed, everything seemed to prime perfectly.
but the engine wouldnt run.... because there was still air in the supply line which caused the injector pump to push air in to the lines going to the nozzles... when this happens the air acts like a spring in there and wont let fuel get to the nozzles. the only way to remedy this is to loosen the lines on the nozzles/injectors and turn the engine over a few times until the air is pushed out and clear fuel is spraying.... then the engine will run.
AND... make sure the fuel shutoff/stop lever isnt sticking in the "kill" position....