You can unplug the EGR motor's connector and see if the issue remains. You can remove teh 3 bolts and clean the EGR as well to make sure the pintle valve isnt stuiuck with carbon.
Bad running can be caused by a bad O2 sensor causing bogging and teh engine to "load up" with fuel when in closed loop. If the issue clears up at WOT, O2 sensors can be the issue. At WOT the PCM doesnt read the O2 sensors, so better WOT running can be indicative of O2 sensor problems.
If its the popets here is the CSFI to MPFI conversion from GM.
CSFI to MPFI - Vortec Engine Fueling Fix - Fuel Injection - Off-Road Magazine
And here is some cleaning info