to test which cylinder is dropping out:
run the engine upto 2000-3000rpm so you can clearly see its misfiring, then remove one injector plug at a time. if the engine starts running worse then you know the cylinder is operating ok, if there is no change to the way the engine is running when you remove the plug off the injector then you know that cylinder is the one causing the problem.
from here you can start narrowing down things to look at, seeings as you have new leads and plugs in it. i would recommend looking at the injectors.
the only other thing that sounds concerning is the condition of your fuel pump, you state that there was fuel in the rail........but pressure and flow are two different things. you might find that there isnt actually ENOUGH pressure/flow to feed the engine when its running. I would try clamping the return line and see if the problem goes away. By doing this you are suppling MAX pressure and flow to the injectors at all times, this will tell you if the pump is no good.
hope one of these things fixes your problem![]()