Actually I mean that in a span of a couple years at most all that happens. If I remember your theory correctly, you said that Ganondorf is first foiled in OoT, then runs off into the desert and steals the Trident. After that he is sealed in the Four Sword and then breaks out and is sealed in the Twilight Realm soon after. That's what I meant. But there's still quite a few other inconsistencies as well, not the least of which being the differences between the Gerudo of OoT and the Gerudo of FSA, as well as the status of the Triforce.
Well, you got it mostly right, but here's the actual theory:
Ganon is an ancient demon. Twinrova reincarnate him in Gerudo form (they are not his mothers but rather his 'surrogate' mothers) named Ganondorf. OoT happens, and at the end Link gets sent back in time and prevents Ganondorf from getting into the Sacred Realm by simply not attempting to get in himself. Ganondorf, having no other way to get into the Sacred Realm (evil ones can't touch the Master Sword) decides to come back to the problem later, after accruing more power. This means that none (or very little) of OoT actually happened in the child timeline (Twinrova doesn't die, the original Sages aren't wiped out, the Gerudo don't turn to evil but instead continue their noble nomadic existence and the new Sages of OoT fame aren't awakened), and Ganondorf continues his 'loyal ally of the king' charade. He turns his attentions to other magical artifacts such as a Mirror in which a dark tribe was sealed...
Meanwhile Link, now a friend of Zelda, is called by her to help her inspect a seal cast over an ancient relic known as the Four Sword. Vaati escapes and FS occurs. Ganondorf seizes the opportunity to steal the Dark Mirror unnoticed while Link is busy with Vaati. When Vaati is resealed, Ganondorf uses the Dark Mirror to force Link to take up the Four Sword again, releasing Vaati once more. While Vaati rampages, Ganondorf steals another artifact he's had his eye on: the Magic Trident. The Gerudo immediately decry him for pillaging a sacred artifact and Link eventually catches up to him with the help of the Shrine Maidens, sealing him in the Four Sword. Link then sets out to find a friend who's been missing for a while and ends up in Termina. What happened to him after saving Termina? Did he ever find his friend?
None remain who know. Thus ends the story of the Hero of Time.
Years pass and when the Shrine Maidens are eventually succeeded by the Sages of TP, Ganondorf is brought forth from the sword so that he may be properly executed. But in an unexpected turn of events, the execution fails when Ganondorf is revealed to possess the Triforce of Power! In desperation, the surviving Sages seal him in the Twilight Realm, but how did he get his hands on the sacred relic?
Was he, as he believes, suddenly 'chosen by the Gods'? If so, little wonder that he's so confident that Hyrule is rightfully his.
Or was it a result of the Hero of Time attempting to travel back with the Triforce of Courage to a time that already had its own Triforce of Courage? This is possible since we know he left his original ToC in the adult timeline - TWW tells us that when he left on his journey through time, the ToC shattered into 8 pieces. Perhaps in an effort to maintain balance, the adult ToC left Link and was replaced by the child ToC unbeknownst to him, keeping 3 Triforce pieces in each timeline but the sudden splitting of the Triforce in the child timeline sent the other two pieces to their respective holders. In this case, none of the 3 would have noticed anything: we already see in TP that Link doesn't realise he has the ToC until his life is endangered, whereupon the ToC activates on its own and transforms him into a wolf. So it's not unimaginable that, all this time, Ganondorf had the ToP and never realised it until his life was in danger.
Either way, the theory's not without merit.