Whenever you see a suffix after the last letter of the engineering number, such as A1 and A2, it means two different vendors are supplying a part under the same part number. The appearance of the part between A1 and A2 can be quite different. On rare occasions, the A and A1 on the part number might occur, but I have not seen it listed this way in the MPC, only on the actual box of the part. There are also occasions where instead of the A1 and A2 on the engineering number, it will have a different letter, such as A, B, and C. For example, C5AZ-6A666-A could be marked C5AE-6A666-A or C5AE-6A666-B. C5AZ-6A666-A1 could be marked C5AE-6A666-A, C5AE-6A666-B, or C5AE-6A666-C.
And it gets more fun. C6AZ-6A666-A was marked C6AE-6A666-B. But, it was for the big blocks in 1966, not the 289. Then in 9-67 (near 1968 production), the C6AZ-6A666-A part number replaced C5AZ-6A666-A. Since these valves were supposed to be replaced every 12,000 miles, the C6AE-6A666-B valves were getting installed on the earlier 289s. And, although Ford did not show different engineering numbers under the C6AZ-6A666-A part number, there were at least two I found -- C6AE-6A666-B1 and C6AE-6A666-B2. Both were different designs, each from a different company.
So, what should you use? You are safe with a C5AE-6A666-A, C5AE-6A666-B, or C5AE-6A666-C marked valve.