The engine could be sucking air and causing a misfire in one or more cylinders.
Look around the engine for a small vacuum hose that may be damaged or unplugged.
Also, with the engine running, listen for a hissing/sucking noise where a hose "should" be plugged in.
Or, tug on each spark plug wire to make sure they're on the spark plug all the way.
well you may want to finish the tune up replace the pcv and egr valves and clean the throttle body, but i must tell you GM had a tough time balancing that motor, they did smooth it out some with the counter balance shaft but still wasn't like their other motors.