See this is what dosen't make any sense to me. Why would MC and FS come first, then FSA a long time later if they all revolve around the same story, same basic "sword power" idea, and same boss. It dosen't make any sense how in MC and FS, Vaati would be the main boss and Link would use the Four Sword to vanquish him, then OoT happen as well as TP, which involves Ganondorf and the Master Sword, then completely abandon the Master Sword and go back to the Four Sword. That dosen't make sense.
Seeing as how MC, FS, and FSA all take place within the same plot, main boss idea, and use the same weapon, I think that MC comes sometime later, maybe even in New Hyrule, followed by FS where we see a different generation of Link, then FSA with the same Link as in FS. That is my opinion. I personally have never heard Miyamoto say anything about FS taking place before OoT, not to say that he didn't, but I haven't heard or read anything at all about that. So as of right now, going with what information I have available, to me it makes more sense for the Four Swords Saga to take place in their own time, apart from the rest of everything thats going on in the Zelda universe, and the only way to do this is to put it before or after everything that has happen. And I've already explained how its confusing to put part of it after and part before, or all before.