Ok, after reading the above:
Since it did it on the old motor too, Give a new fuel filter a try, at least get that out of the equation. As a suggestion, from personal experiance, alot of the stock fuel filters for our trucks changed to the newer, updated design, including the AcDelco one. I had problems with the updated ones, i belive they are too restrictive and caused fuel starvation and that produced a rattleing sound at certain RPM's. With the old type filter, I had no issues. The current filter I run is a Baldwin, the old type still. I would recommend one! To tell "old" VS "new".... the new type has 4 kidney bean shaped holes in the middle......crappy
The good old type has 2 rows of holes, horizontally in the sides of the inside edge. Make sure that your plastic filter bleeder screw is in good shape and not broken/cracked. And also no fuel around the primer pump
Baldwin# BF7827
Attatched a picture of the old "good" type filter!
Since these trucks have no electric pump to help feed the main pump, it has to suck the diesel all the way from the tank and through the filter and to itself, so a dirty/restrictive filter=problems
(my problems i learned from were all before i installed had a lift pump on mine)