Slant factory performance

First thing to keep in mind. The 1960-1967 slant six (and small block) had a smaller pilot hole in the back of the crank, than the 68 and newer engines. Therefore, you cannot use this engine in front of a 1968 or newer automatic transmission, without a special/custom torque converter.
Head flow and exhaust manifold does not really make enough difference to be concerned about. However, while the head is off the engine, I would have it milled to raise the compression ratio, and get a quality valve job done. Over size valves and some porting will help, but without doing other work, such as a cam upgrade and/or more carburation, I don't think it is worth the money, unless the valves need replaceing, anyway. Factory manifold would be a super six (2bbl) (but they are getting pricey) aluminum if possible. Low restriction exhaust system on the vehicle.