I love reading stuff like this. I'm always interested in other people's views on the storyline.
Anyway, might as well give some insight to things I've noticed.
So browsing through Wikipedia, I came across a chronology of sorts. Other than what has been said (of the two timelines), it says what games predate what games.
http://en.wikipedia.org/wiki/Legend_of_zelda
Essentially, Link to the Past predates the first Legend of Zelda and Zelda 2, which we know the first two games are of the same Link. Ocarina of Time, which we already know, predates those games and sets up the split in the timeline, with Majora as the direct sequel to OoT in the Child Timeline. TP is in the child side, set 100 years after, and WW/PH is set hundereds of years in the Adult timeline, and it says ST will be set 100 years after PH. What is interesting is that Aonuma states Minish Cap, Four Swords, and Four Swords adventures take place BEFORE Ocarina of Time. So that kinda skews what's already been said.
But things I've noticed...I've recently been playing TP again, and one thing I thought was interesting. I honestly think that Ganondorf is actually the OoT Ganondorf. It's said that when Link when back in time, they arrested Ganondorf and sentenced him to death. Obviously they could not, as Ekul has pointed out already. So while one Ganon was trapped in the Sacred Realm, one was trapped in the Twilight Realm. But Ekul pointed out the Prank by the goddesses, set when Ganon escaped the Sacred Realm, probably a few years or decades after. So how does it pick Ganon in one timeline when the other is picked years earlier? My theory is how it's always a Link, always a Zelda, always a Ganon that is picked. But more than that, it's how even seven years ahead of time, both Young Link and Adult Link can have the same gear. Because they are always picked, the year seperation does not matter, only the fact the triforce is split, and it picks their own bearers.
One last thing, in WW when you are within the area of the Master Sword, all around you are glass windows showing the 6 sages from OoT. However, in TP, they are all wearing masks, and are said to be the wisemen who were the teachers of the Royal Family. I think this has to do with the sages being awakened in the Adult timeline, yet were not in the Child timeline. So maybe with any future games, we can figure out the timeline based on who's considered the sages?
That's my two cents. As for what game goes in what order, you got me. What you guys stated is pretty good already, besides the whole Four Swords and Minish Cap sagas set before OoT, as stated by the director. And I do think this sleeping Zelda in Zelda 2 is the first Zelda, born before any of the other Zeldas. I do think the back story of Minish Cap is the first, followed by the sleeping Zelda story, then probably Minish Cap, the Four Swords Saga, then the OoT split, and your guess after that is as good as mine.