Here is a hint.
This is hard to communicate here, but if you mean that your truck starts to miss and carry on like it is cold after 2000 rpm, I would bet that if you pulled out your flow valve and shake it, it will rattle a little, or you can poke the ball inside and feel that it doesn't seat right, or you could hook up a fuel pressure guage to your injection pump, and you would see a lot of spikes, erratic pressure, and pressure that does not meet the min standard at rated rpm... . 25 psi min, and a "good" 25 psi at that, not running all over the gauge. This is just a hunch, but if your fuel shut off is opening all of the way, then I would bet on the flow valve being the next in command, easy fix, common symptoms for the most part.
Hope this helps,
Russell