Phil, when the pump was swapped, was the housing it bolts up to and the big gear inside it removed? If gear and housing were left undisturbed, and you only removed the pump, with the marks lined up it should not be out of time.
Every time I adjust the fuel screw (twice this week, turning it down), when I put everything back together I crack the injector lines open at the injectors (loosen the nuts a bit, obviously don't remove them completely) and I give it two good 15-second cranks so all the air that's inside the line gets purged, you should see fuel coming out from around the line nuts at that point. Tighten nuts down, fire up truck, she'll be jumpy a bit, but after a minute or so she stabilizes the idle and she's good to go.