Has the throttle position sensor been replaced? I THINK those have a potentiometer that could have a bad spot in it around that position at that rpm.

 

I know you have a new pump but have you checked the pressure?

 

Way I read it is this, at point A it is fine, then at 2k rpm, rough, but then it smooths back out at some rpm higher than 2K, so A|-------|B it runs fine at anything other than that slot between A & B? If that is the case, I'd think the TPS reference signal could be the issue. Not familiar with todays cars that well, but electronics are still the same. That 5 volt signal reading back from the device to the PCM has to have a variable resistor that changes with movement (potentiometer) I have seen this as a classic example of the wiper or other componet (worn, cheap) causing problems in transmitters.