Air intrusion almost certainly. Start there before you try anything else. A good test, put some clear fuel line between the lift pump and the filter head. Start it, and see if you get bubbles in it, also rev it up some and watch. Air's compressibility plays havoc with how the mechanical system times its injection points, and will play merry hell with how your engine runs.
Your truck also had the Stanadyne water separator in it. This is a notorious source of air intrusion. There's even a tech article here about it.
http://www.oilburners.net/forums/showthread.php?18212-The-Stanadyne-Water-Seperator-Exposed
As a test you can also try bypassing it, or plugging the drain hole on the bottom, and seeing if that changes anything. (do not run it long without some sort of water separation system. If you get water in your IP, you will kill it)
Incorrect timing will not give you the symptoms you're talking about.
however, I had a problem with my advance piston being sticky. Would cause random power surges while accelerating when it would unstick. Was lucky, and after a week of letting it stew in ATF overnight it went away. (everything on this truck was filthy, even the internals apparently)