CAT 3406e fuel problem

Ok a few weeks ago I had 2 injectors replaced truck has not ran right since I even took it into CAT to have it looked at.
They said the 2 that was just replaced ran a bit weak and fuel pressure was a tad bit low.
Then they ran the rack showed me blown manifold gaskets. Got new gaskets and it still seemed rough.
Last weekend started the truck ran home to get something got back Truck was dead and would not restart primed it and still would not start so used a bit of starting fluid it ran rough off and on all week. Last night started it ran about 10 then died. Starting fluid ran fine for a another 30 min went home. Thought let's check it out so went ahead and started it up again 15 of idle sometimes smooth others rough then real rough and died.
Pulled the water separator it's less than half full? Where should I start looking?
Motor is a Cat 3406e in a T2000.

 

Ok pulled filters and replaced them and got it running and found a hose saturated so replaced all seems well now. Guess a mix of bad filters and a hose allowing in air.

 

Well take that back ran great all yesterday and this morning started acting out of fuel again put it 1300 rpms 20 sec later smoothed out back down to 800 5 min later running rough back up to 1300 smoothed out been at 800 for over 15 min still smooth.
So break down is check for bad wires to ecm and check valve and hope it's not the transfer pump.
The injector harness is fine CAT looked it over real good when they had it apart.
edit new info
Oh and the hand pump was just replaced wait umm same time as the injectors and not able to get it to pull any prime?

 

So pull the return line and see it its get bubbles of air? How steady should the return flow be?
Is that a repair that really needs to be done at a CAT shop?

I will be following up on each suggestion this weekend and just trying to get idea on what each will involve. Will test out myself just spent a grand getting it diagnosed and for CAT to find what's wrong with no luck don't mind spending the money as long as get results lol I know some times it like that though just trying to keep it to a minimum.

To be honest this sound very likely because when it runs rough it seems almost like a blown injector. When 1 and 2 went it sound almost exactly like it does now off and on. Just not smoking