What intake manifold do you have? I have seen similar problems with cannon intakes. Dead cylinders at idle and/or major flat spots or hesitations. The issue with cannon manifolds is they have a port that connects all the cylinders together. This is a bad design choose as intake pulses from each cylinder are able to interfere with adjacent cylinders. The solution to this problem is to weld the ports up between the cylinders, or change to a better manifold, like a TWM