Are you wanting to replace the Cruise-o-Matic with a manual transmission or are do you want another automatic?
Either way, the first thing you need to look for is a transmission (automatic) or bell-housing (manual) that will bolt up to the back of a Ford FE engine. From there the choice of transmission ought to be pretty straight-forward.
If you are asking were there any other automatic transmissions offered by Ford in 1962, as I recall during those days there was just an "automatic transmission" option, so if I had to guess I'd say that the original offering was probably just a "Cruisomatic". By the time 1972 came around there were FMX and C-4 and C-6 automatics and Ford made the decision which one to put where...if you wanted an automatic you just put a check mark on that option, paid your money, and waited for Ford to send your car to the dealer. There was, to my knowledge, no manner in which a choice of automatic transmission was offered.
Admittedly, 1962 was just as I was beginning to develop an interest in cars, so there is a fair chance I could be wrong. If I am I hope some of the more knowledgable members will correct me.
Cheers!
Dugly