I had a very similar problem in my truck a couple years ago. It didn't smoke on me but it shook a lot and wouldn't rev over 2k rpm. I took it to a private shop and and they tested it and it said one of my injectors was bad. I ended up taking it to a dealer for a second opinion (the guy was trying to rip me off) and it turns out that it was the fuel injector wiring harness had a broken wire so one of my injectors wasn't working. Then last year the other wiring harness went out on me and my truck was smoking like crazy when I started it because the glow plugs on the passenger side weren't working. Just a thought if you haven't checked them already

 

That man is far from "the man"... maybe in his own mind...

 

Well the injectors are in and the truck runs great, only thing is it sounds like its starving for fuel at times. Is that normal for stage 2 sticks? I havnt got my custum tunes yet, just been driving on stock setting.