I may be going through the same thing as you are. Not really missing, but a slight fluttering hesitation/surge under light throttle from 1600-2000 ish rpm.
I found corrosion in the plug between my Comp MAP output and the truck's harness. I didn't clean it out very well (remove, insert, remove, insert, etc x10) and the surging went away. That was about two weeks ago and now the surge is back. I have some new plug ends that I'm gonna put on this weekend, so I'll let you know how it turns out.
Not counting a bad VP44 (which would probably have other symptoms too, but maybe not), there's really only a couple of things that could effect the fueling amount on these trucks. The APPS, MAP sensor, and the IAT sensor (and of course all their connections). In my case, the ECM was reading an intermittant low signal from the MAP due to the corrosion (no code since it didn't have an open circuit and the voltages were still within the range). And if the ECM doesn't see boost, it won't give (as much) fuel. Any noise in the MAP signal will result in changes in fueling, similar to twitching the throttle.
Check your connectors (MAP and IAT); hopefully you'll get lucky.