The Next Wii Zelda

[WiteoutKing]

For example, at one point Miyamoto claimed that the series went: OoT, Zelda, Zelda 2, and then the Adventure of Link.

...Zelda II IS The Adventure of Link.

If you believe the split timeline, then Majora's Mask immediately follows Ocarina of Time in the split timeline. The timeline Link left This then leads to Twilight Princess.

The Link from Ocarina of Time is a different Link from Twilight Princess.  OoT Link leaves Hyrule and enters Termina.  It is unknown if he ever escapes that dimension.  The plot to Twilight Princess involves Ganondorf being arrested, and sent to the Twilight Realm, as opposed to the alternate timeline (where the last half of OoT happens), which has Ganondorf being sealed within the Sacred Realm.

I'm sure you beat Ocarina of Time. Link left with the Master Sword when he was transported away.

My mistake.  He does take it back.  He places it back into the Pedestal of Time.  That said, what happens to the Master Sword when Link goes backwards in time normally?  In the past it stays in the Pedestal of Time.  In the future, it stays wherever he placed it (which is normally the Pedestal of Time.  At the end it happens to be the ruins of Hyrule Castle.)

Link DID kill Ganon at the end of Twilight Princess.  [...]  The only way this really fits on a timeline is if it's after Wind Waker, which contradicts an earlier statement that it's between OoT and Wind Waker.

You raise a good point that you probably didn't intend to.  In WW, you hear the legend of OoT's Link.  Which means that this is in the timeline where the last half of OoT happened.  TP exists in the timeline where MM happens instead.  That said, it's a bit vague exactly what happens to Ganondorf.  It seems strongly implied that Ganondorf is dead.  The Triforce is gone, his connection to Zant is severed, and he is not in the Twilight Realm where he can survive.  It could be the last time Ganondorf is seen in that timeline.

The timeline effectively looks like this:

NL = New Link
DS = Direct Sequel
1. Ganondorf is defeated by Link and Zelda, and sealed by the seven sages within the Sacred Realm.
2. Ganondorf is arrested by King Hyrule, and the six sages (no Zelda present, one also dies) imprison him in the Twilight Realm.
3. Ganondorf breaks free from the Sacred Realm, and no Link shows up.  Hyrule is flooded.
4. Ganondorf is impaled through the head, and turned into a statue.  From here on he is unable to take human form.

 Once again you bring up a point you didn't mean to.  At the end of the Adult Timeline if OoT, Link disappears.  The gods could very trivially "hold onto" the clothes and then give them to TP Link sometime later.