Having read through this thread twice, and pondering it for two cigarettes and a glass of iced tea, I think I may have something. You said in previous posts that most of the fuel system has been replaced, and that you have good fuel pressure KOEO, KOER, and no bleed off after the key is turned off. My question is this: have you ever checked your fuel pressure while the truck was acting up? My guess would be no, because you always seem to have the issue after running it or driving it for a while and letting it sit for a bit. This still sounds like a fuel related issue, so I'm going to suppose that the fuel pressure is bleeding off, likely through an injector, and causing a hard start (due to loss of prime) and rough idle (due to loss of prime and a rich/flooded condition) on startup. I would suggest cycling the key several times before each startup. If the issue is resolved, or at least changes from a hard start to an initial rough idle, then you'll have a clue as to where the problem lies. A more scientific way to do this would be to leave the fuel pressure gauge connected to the rail, run it up the cowl, and tape it to the windshield. That way you can actually see if the pressure is bleeding off while the truck is sitting and then start diagnosing where the fuel is going. If you've tried it, it may be worth another try. If you haven't, it's a pretty simple way to get some new data.
