do u have adjustable cam gears??? if u do it could just be the way the gears are set. if u set em right itl increase overlap and the car will idle rough like that. u could try to adjust the idle screw on the throttle body n c if that helps. if not id say to unplug ur ecu n plug it back in so itl re learn its idle (computers are funny like that). if that doesnt help i dunno what else to tell ya. could b an iac or a tps........lots of things control ur idle.