The New FFIV

To create another magic menu you would need to replace the target command's menu creating code (there's some code in the C1 bank that creates the menus for magitek, lore, rage, dance and other commands) along with other data I'm not sure of now :p.

A wild guess to create a command like twincast would be something like this:

Have two characters share the twincast ability. You would need to have some lines in the code (C1 & C2 banks) to specify the ID of the two characters sharing the command. You would also need to have both of these character's active bars fill at the same time. The damage formula for the twincast ability needs to be redone, since you have to take into account each character's magic power to calculate the overall damage of the resulting spell.

Also, you would need to define when is the command going to be available in battle (kind of like the runic command). Will it be unusable if the character is silenced, imped or has no magic spells?

I think lenophis is the best to provide info on how to do this, I'd ask him if I were you, he may be able to provide more insight. You have his MSN or skype?