Indeed, there are quite a few possibilities in terms of how to arrange such a combination. Off the top of my head, I would imagine it as something like this:
Assuming six Zords, Twilight's zord would be the body/head, Applejack's and Pinkie Pie's would form the two hind legs, Fluttershy's and Rarity's would form the two front legs, and Rainbow Dash's would form a pair of wings. It's also possible that you could have AJ's zord form both of the back legs, thus freeing up one zord to serve some other purpose as needed, such as additional body armor or a weapon.
At any rate, keep up the good work! ^_^