I'm just gonna structure your timeline like this so I can read it better when I reply here (to give me something to look at).
.....(AT)......../--WW/PH--ST
MC--FS--OOT
......(CT).......\MM--TP--FSA/ALttP/LA--LoZ/AoL
The first problem I see here is that you have ALttP as a direct sequel to FSA. I've never seen that in a timeline before, and here's why. In ALttP, Link does not seem to know Zelda until he meets her in the castle dungeon, and vice versa. Also, there is no mention of Link doing anything prior to the events of ALttP. That tells me that they are obviously different generations of Link and Zelda from FSA.
I cant remember exactly but the theory is that when Link is sent back in time he takes the ToC with him meaning there is no ToC on the AT so nobody can obtain the ToC, something like that.
Well that wouldn't exactly work, seeing as how the ToC is obviously in WW. Being that WW is widely believed (and by you as well) to be on the AT, that would put an end to this theory pretty quick. My own personal opinion of the matter was the Link did gain the ToC somehow as a kid, which I believe was by fate and not from him going through time. The way I see it is Link was sent back through time to a point before he pulled the MS out. So like Ganondorf recieved the ToP mysteriously in TP, Link did so at the end of OoT with the ToC. However, when Link went to Termina, he lost his piece of the Triforce. That's my theory anyway.
I dont personally believe that FS is a direct sequel to MC I believe it takes place sometime after MC. I believe sometime passes between FS and FSA also meaning I believe there are three Links or Heros and three Zeldas.
I agree. I don't like to get into the Four Sword Saga much, just because its so controversial amongst timeline theorists and in my opinion they are really more of a side-quest set of games than anything else, but I believe that MC happens whenever, we'll just say first, then FS happens sometime later with a new generation Link. Actually, I would put FS before FSA as a prequel to it, judging by the intro to FSA, which makes it seem like the Link and Zelda from FS and FSA are the same by identifying them by name, whereas when it talks about MC's Link, it just refers to him as a Hero.
So what your saying is ALttP ends and the triforce is whole, the King then obtains the Triforce and passes parts of it to the Prince and Zelda, Zelda is sent to sleep and the wizard dies. They name every Zelda - Zelda in her honour. Eventually The Triforce splits because of Zelda and Ganon and its reunited for the start of OoX. Actually I believe the Legend of Zelda "The BS not the game" takes place at the start of the timeline cause otherwise why would all the other Zeldas be called Zelda if its not a proclomation till the very end.
I think that was basically what Zelda 2 tried to set up, but there's also the fact that it was the second only of many Zelda titles released. Over time, I'd say the developers kept this story in mind, but didn't follow it strictly. The fact that Zelda is somewhere in a Palace throughout the entire history of the Zelda series, all the way up until AoL, but no game has any mention of her, is kinda odd to me. I think they just wanted to give a reason why the Zelda from LoZ was named Zelda, and to show that the one from AoL was a different one. So far, no game has ever followed up on the BS to AoL, so I think that the whole plot there would explain a lot, but has too many holes in it to be very credible to any other game titles.