Closed emissions means that in addition to the PCV setup on the RH valve cover that has a hose connected to the base of the carburetor, there is a hose from the LH valve cover oil filler cap to a fitting on the front of the air cleaner (the HP hose goes under the base and attaches to a fitting there). Open emissions means that there is no second hose to the air cleaner. A closed emission setup is required for California smog 66 and on. This applies to 2V and 4V engines. Road draft tube engines are a whole different setup.
I have a C5OE-9425-G manifold (D/C 5C9) on my 65 GT Fastback (eng assy D/C 5G10T), and a C6OE-9524-B (D/C 5G27) on my 66 GT K Fastback (eng assy D/C 5H23Z). The differences in manifolds are the 65 has a small temp sensor hole and the pad to the rear of the carburetor is not drilled and tapped. I have the bell crank type kick-down for the C4 AT. The 66 intake has a large hole for the temp sensor, three holes drilled and tapped on the pad to the rear of the carburetor for the smog bypass valve and the same holes (although unused) for the AT kickdown. The date for the temp sensor (C5DZ-10884-A & C6DZ-10884-B) change-over is 9/1/65 (Sec 106 pg 17 Ford Car Parts). I would think that the manifold application date would be the same.
Remember, the casting number is just that - a casting number. The manifold was then machined for multiple applications and received a different (unmarked on the item) part number. The service part number for all 1964-68 289/302 4V applications (ex GT-350) is C4OZ-9425-H so it must have the large hole temp sensor and all possible accessory holes drilled and tapped. It's casting number should be C6OE-9425-B (or C8AE-9425-B, the latest p/n).
Jim