The "red box" looks to me like a manifold vacuum fitting that is plugged off. The "yellow box" looks to me like one of the screws that holds the choke housing to the carb, but looking again, guess you mean the vacuum fitting/line. I believe that is ported vacuum to the distributor but may go through a TVS before it gets there in the correct configuration. The carb vacuum port should certainly appear on the vacuum diagram. The other port should appear as manifold vacuum.