I am going with droptop on this one except he left out one important problem with headers vs manifold which is plug access, some headers make changing spark plugs a complete nightmare. I have polished a lot of stock manifolds to get better flow and have always been satisfied with the results. You can mirror polish exhaust ports and manifolds to get a smoother flow, and less carbon build up but you will need a dremel with flex shaft, inspection camera, a lot of grinding and polishing stones, and a hell of a lot of patience. Oh and you can smooth up intake ports as well but DO NOT mirror polish those.