3406b missing allen screws from pump??

Trying to help you diagnose the problem, but with issues like this it's hard without seeing and hearing the truck. What's your smoke situation when it's running right and running poorly? Is there a noticeable difference in smoke or how the motor feels (smoothness wise). I have a couple ideas on the problem but I want you to get all the quick fix easy things out the way b4 you start really digging into a more serious issue.

 

What is your status on the Afrc valve? How black of smoke, and does it clear or just keep beveling black smoke on a climb?

 

If you want to temporarily disable the AFC, take a 9/16" shallow 3/8" drive socket and put in the cap that comes off the AFC that the air enters into, put the open socket side towards the shaft, this will depress the rod and allow full fuel

 

Well don't take it apart, back out the adjustment screw first and see how it clears the smoke. When you back that all the way out, you should have almost no smoke. If your still throwing a lot then something's up with that valve. Now, this doesn't effect boost a whole lot, however, if it's not working right it could. Also, the line that comes off the block and to that valve is important. I would take that off and clean it, it is a very simple job but I had a buddy who had a clog in that line and it created these symptoms.
I was thinking timing but if the truck is running smooth then it's running smooth I would leave alone.

 

SmokinCat, doesn't his symptoms seem kinda odd, the way it comes and goes? It makes me think it's something stupid, and a simple fix.