Howard,
I want to know, what on earth did it turn out to be wrong with the truck?
I praise god that the truck is running great now. Believe me man, your vehicle is not the norm, never ever heard of one having such problems, but glad it's running good now.
Probably the best thing you could do at this point, to reduce your smoke, assuming everything else is good, would be to at the very least, cut out your muffler, or get a Walker Big Truck Muffler (quite cheap and is not loud) that is straight through design.
now that you have full gauges, what are you seeing for boost 20ish # right?
As for your intake, you could always custom make one out of exhaust tubing.
Even if it connects to the stock air filter box, if you get rid of the rubber with all of the ribbing and such that restricts airflow, that would also help. I forget where the E-series gets it's air from. Would it be possible to do a zoodad mod?