I'm not expert and may have overlooked a million major/minor things but this is sort of a way to show how MC-FS-FSA could be fit into the Imprisoning war/Ocarina of Time events.
Assumptions
The only assumptions important to note is that the Twilight Realm and Dark/Sacred Realm are two different places. And the Dark mirror, while used to create Links in the Light/Normal World, was also like magic mirror from ALttP, though applied to the Twilight Realm, not the Dark Realm. Obviously Ganondorf would not have known about its transportation power from Twilight realm to the Light realm because it does not transport you from the Light realm to the Twilight Realm, but only from the Twilight Realm to the Light Realm. So Ganondorf would not have discovered this power UNTIL he was in the Twilight Realm.
Ocarina of Time - Link is sent back in time and proceeds to tell Zelda and the King about Ganondorf's evil. Ganondorf had obtained the Trident and Dark Mirror at this point already, as told about in FSA. The trident gives him power in OoT to follow Link into Sacred realm and obtain Triforce. This same sequence of events happen but this time the Ancient Sages use it as a trap. They wait for Ganondorf to emerge from the Sacred realm, having already touched the Triforce. He kills one of the sages but they send him into the Twilight realm using the Mirror of Twilight.
Minish Cap - Vaati appears and begins to wreak havoc in Hyrule. Young Link, already friends with Princess Zelda, stops him, not with master sword, because it is the seal on the sacred realm which Link doesn't want to open again. So he needs the Four Sword.
Four Swords - Occurs shortly after Minish cap and it is still within the seven year period.
Majora's Mask -Looks for Navi while everything in Hyrule seems fine.
Four Swords Adventure - Ganondorf had let himself out the Twilight Realm using the Dark Mirror almost as soon as he had been put in it, though he did meet Zant while there. He wanted Zelda's "lightforce" or triforce of wisdom for himself, because he need all three pieces, so he let Vaati try to obtain that unwittingly. He thought that if he reappeared himself he would be sealed by the Ancient Sages wihtout his Dark Mirror leaving no escape. He is eventually found out and defeated and sealed in the Dark/Sacred realm, not the twilight realm, by the power of the four Sword. The adult ending of Ocarina of Time never occurs obviously because Link changed the past. Link does remember it however because the events did happen and stayed within his memory. He passes this legend along with the rest of the story. Perhaps Zelda did not send him back in time to change the events until he had defeated Ganondorf because 1. She was hiding as Sheik and could not use her real power in that form 2. Was captured the moment she revealed herself.
Twilight Princess - Ancient sages scene shown is the young Link capture story. Zant met Ganondorf when Ganondorf was first sent into the Twilight Realm. Beginning the whole Twili revolution/Zant event thing to start. When Link draws the Master Sword to save him from his wolf form, he unwittingly opens the door to the Sacred realm/Dark realm where Ganondorf had been trapped by the power of the Four Sword. Perhaps sealed in Dark Realm again leading up to Link to the Past.
So Basically the timeline would look like
OoT game version - OoT changed version - Minish Cap - Four Swords - Majora's Mask - Four Swords Adventure - TP and so on.
Assumptions
The only assumptions important to note is that the Twilight Realm and Dark/Sacred Realm are two different places. And the Dark mirror, while used to create Links in the Light/Normal World, was also like magic mirror from ALttP, though applied to the Twilight Realm, not the Dark Realm. Obviously Ganondorf would not have known about its transportation power from Twilight realm to the Light realm because it does not transport you from the Light realm to the Twilight Realm, but only from the Twilight Realm to the Light Realm. So Ganondorf would not have discovered this power UNTIL he was in the Twilight Realm.
Ocarina of Time - Link is sent back in time and proceeds to tell Zelda and the King about Ganondorf's evil. Ganondorf had obtained the Trident and Dark Mirror at this point already, as told about in FSA. The trident gives him power in OoT to follow Link into Sacred realm and obtain Triforce. This same sequence of events happen but this time the Ancient Sages use it as a trap. They wait for Ganondorf to emerge from the Sacred realm, having already touched the Triforce. He kills one of the sages but they send him into the Twilight realm using the Mirror of Twilight.
Minish Cap - Vaati appears and begins to wreak havoc in Hyrule. Young Link, already friends with Princess Zelda, stops him, not with master sword, because it is the seal on the sacred realm which Link doesn't want to open again. So he needs the Four Sword.
Four Swords - Occurs shortly after Minish cap and it is still within the seven year period.
Majora's Mask -Looks for Navi while everything in Hyrule seems fine.
Four Swords Adventure - Ganondorf had let himself out the Twilight Realm using the Dark Mirror almost as soon as he had been put in it, though he did meet Zant while there. He wanted Zelda's "lightforce" or triforce of wisdom for himself, because he need all three pieces, so he let Vaati try to obtain that unwittingly. He thought that if he reappeared himself he would be sealed by the Ancient Sages wihtout his Dark Mirror leaving no escape. He is eventually found out and defeated and sealed in the Dark/Sacred realm, not the twilight realm, by the power of the four Sword. The adult ending of Ocarina of Time never occurs obviously because Link changed the past. Link does remember it however because the events did happen and stayed within his memory. He passes this legend along with the rest of the story. Perhaps Zelda did not send him back in time to change the events until he had defeated Ganondorf because 1. She was hiding as Sheik and could not use her real power in that form 2. Was captured the moment she revealed herself.
Twilight Princess - Ancient sages scene shown is the young Link capture story. Zant met Ganondorf when Ganondorf was first sent into the Twilight Realm. Beginning the whole Twili revolution/Zant event thing to start. When Link draws the Master Sword to save him from his wolf form, he unwittingly opens the door to the Sacred realm/Dark realm where Ganondorf had been trapped by the power of the Four Sword. Perhaps sealed in Dark Realm again leading up to Link to the Past.
So Basically the timeline would look like
OoT game version - OoT changed version - Minish Cap - Four Swords - Majora's Mask - Four Swords Adventure - TP and so on.