For 66 Bob Mannels book (pages 6-31 and 6-32) states that the vacuum port was either plugged or had one of 2 fittings.
One would be a 90 degree threaded fitting for cars that had either power brakes only or automatic transmission only and nothing else. The other possible fitting would be the one jwc66k posted in the picture above. This fitting would be used with cars equipped with any combination of thermactor emissions (small hose port), vacuum operated accessories (large hose port), auto trans and/or power steering (threaded port). In the case of auto trans only equipped mustangs, a section of hard tubing that was shaped around the contours of the air cleaner and narrowing at the top was used for connecting it with a small piece of rubber tubing to the auto trans modulator hard line. If power steering was installed a different tube as was installed like in the picture I posted (same as 65) with a rubber line connecting from the end of the tube to the power brake booster. If both auto trans and power steering was installed, Ford always used the tube for the power brake booster and the auto trans modulator picked up its vacuum source from a fitting on the power brake booster. The Mannel book does not point this out but I'm assuming unused ports were plugged.
Do yourself a favor and pick up a copy of Bob Mannel's Mustang and Ford Small Block V8 book (1962 - 1969). There were so many details like this and running changes covered in this book, it makes it worth it's weight in gold. In my opinion it's indispensable for getting things correct.
Mark