Yeah, that might be the easiest option, but it would be cool to have a Flying V kit where the Floyd routing has already been done, if you were to install a Floyd on a standard Flying V kit you would also have to sort out the nut-shelf so that the locking-nut sits on it properly, or alternatively, you would need to install a Kahler Locking-Nut.
The other issue I can foresee is with the neck back-angle, it may need reducing to allow the action at the 17th fret to be set up right without having to raise the two pivot-posts too high.