That rear port has a hose that goes to the bypass valve assembly located on the intake manifold at the LH rear. Apparently Ford used that type of air cleaner assembly in 1966 for non-smog applications as I have a few with a rubber cap over that port. For a complete installation diagram, I suggest you get a set of 1966 Mustang Assembly Manuals published by Jim Osborn Reproductions and sold by most Mustang part suppliers. The set for 66 consists of Body, Electrical, Interior and Ford Engines, plus get a 64-65 Chassis Manual as there is none for 66 - yet. The books are in the upper 90 percent accuracy level, plus they give you a place to "red line" in corrections. For example, my electrical book has the harness ID tag locations noted. The 64-65 Chassis is about 50-60 percent accurate for 66 but is better than nothing.
Jim