When in doubt, read the book.
Per the 1964 Mustang Electrical Assembly manual (AM0003) pg 11, there were three batteries used for standard assembly line Mustangs:
C3DF-10655-E, a 40 amp-hour for 170 CID I-6 engines;
C3DF-10655-G, a 55 amp-hour for 260/289 CID V-8 engines;
C3AF-10655-N, a 65 amp-hour for Regular Production Option, Z-106, V-8 engines (option Z-106 is heavy duty battery).
I'm not sure about battery filler cap colors, but I believe the 6 cylinder ones were yellow, the standard V-8 were yellow and the heavy duty were red. A green cap signified no acid had been added.
Per the 1965 Mustang Electrical Assembly Manual (AM0008) pg 11, there were two batteries used for standard assembly line Mustangs (the same information is in the 1966 Mustang Electrical Assembly Manual (AM0013) pg 16 for 1966):
C5AF-10655-A, a 45 amp-hour for all engines;
C5AF-10655-B, a 55 amp-hour for option Z-106 (shown as O-106), as "heavy duty battery option".
I believe the standard battery caps were yellow and the heavy duty caps were red.
See the attached chart below. The only correlation is size and amps. Prefix letters indicate cap color.
Service apparently sold all three types for at least the 10 year federal mandated replacement requirements. The Mustang aftermarket "trimmed' the selection to "practical" sales.
Jim