Since I didn't a section for GameCube games, I figured this was the most appropriate place for my question. Let me know if it should be somewhere else.
SPOILER COMING
I was reading a Zelda Characters FAQ which said that in Four Swords Adventures, "It states that Ganondorf was born and raised in a town of the Zuna in the Desert of Doubt." But then I read a game script of FSA dialogue, and in that I see repeated references to Ganondorf being a member of the Gerudo tribe. Can anyone tell me for sure what FSA says about Ganondorf's origins? I am trying to determine if/how much it contradicts Ocarina Of Time's origin for Ganondorf.

He is a member of the Gerudo. The Gerudo didn't want him as they finally reached a reputation of being peaceful. They remembered what happened the first time. This game doesn't not contradict Ocarina of Time at all. This is a second Ganondorf, being reincarnated. (He died in Twilight Princess). The Gerudo tried to stop him from Reaching the Desert of Doubt. He obtained the Trident of Power and transformed once again into the Demon King Ganon. (Like he did in Ocarina when he got the Triforce of Power).

He also broke several of their laws trying to reach the Desert of Doubt.

This is why I don't like Zelda timelines

The Faq made a mistake. What is it you don't like Bloodysaber.

LOL, well, timeline issues aside for now (although you REALIZE that's why I'm doing this research), I primarily want to confirm whether this "Zuna" reference actually appears anywhere, or if that guy was somehow very confused. I have never heard of Zuna. I'm not even clear whether he means it's a place or a people. Sadly, I never completed FSA myself, as it seemed most fun on multi-player, and I couldn't get a consistent partner to play it with.

EDIT: Thanks KaiserGX, I see you clarified the answer I needed while I was correcting spelling
So, is it widely accepted by fans that FSA Ganon is a reincarnation? I only recently discovered that some claim he was permanently in "pig-form" after a certain point.

Now tell me how adult Link got his tunic in OoT, he was frozen for 7 years, I'm sure clothes don't grow.
Wouldn't he just rip out of his clothes? where did he get that new tunic?

and also, how did TP Link get the green tunic too if the last link was still wearing it when he left hyrule in Zelda MM!
And he never found Navi in Zelda MM, so that stroy never ended!
It just doesn't add up!

The game itself says he is the reincarnation of a previous Ganondorf. Also the Japanese Historia Book mentions this.
•The Gerudo Thief Ganondorf’s Reincarnation

Hundreds of years passed since Ganondorf’s defeat. The relationship between the Gerudo tribe, Hyrule Kingdom was restored and peace returned.

However, a new Ganondorf was born. Ganondorf defied the laws of the Gerudo village and invaded the ancient pyramid and took the wicked weapon called the “Trident.” Then, to bring darkness over Hyrule, he stole the Mirror of Darkness from the temple in the forest.

•The Scheme to Obtain the Power of Darkness

In order to cover Hyrule in darkness, Ganondorf stole power from the people. First, he set his eyes on reviving the sealed Wind Sorcerer Vaati of the Force Era. Then, he created a Shadow Link with the power of the Mirror of Darkness and threw Hyrule into chaos.

Zelda says this at the end of the game.
"Ganon...This beast was once of the Gerudo...Once human. He was called Ganondorf! King of Darkness, ancient demon reborn. The wielder of the trident!!" ~Zelda

Rauru changed his clothes. Given the Ghost of the Hero of Time in TP, it shows he lives a lot longer. He became a full Knight of Hyrule (with new armor) as he put his old clothes away. The story in TP tells you what happened to MM's Link. He failed to find Navi.

I'm trying to see how far I can get without doing a lot of conjecture. I wouldn't mind separate timelines, separate series's, but one thing that really gets to me is the idea that anything could happen in between OOT and ALTtP. That makes me crazy.
I always assume that just because something is left unsaid, that doesn't mean it didn't happen, but I try to avoid adding extra complications in the process of trying to solve main points.

EDIT: I also don't feel the need to explain things that are, to me, obviously just a function of it being a game. Although, people sometimes have fun answers to that stuff too.

Just focus on what does happen. No one really knows what happens until it's revealed by Nintendo or it touches upon it in another game.

Just remember all the games (except for obvious stuff such as Melee, Link's Crossbow Traning) are part of Hyrule's History. None of the games ever do a "reboot".

Yeah. Honestly, when I thought FSA broke continuity, and I learned it was made by CapCom, I was a little gitty at the chance to write it off and have one less puzzle piece to sort out. But, as I've learned from you, not only is it legitimate, but it's pretty interesting too! Now I might have to find whatever closet/box it's in and play through it. Heck, I've already run through like four of the others since I beat SS.
Anyway, I'm sorting out a priority list for what I consider canon, so far it looks like this:
1. What is said/seen in the games in the present of the player
2. What is said/seen in the games in back-stories (opening sequence legends)
3. What the manuals say
4. What Nintendo says
5. Fan consensus

Also, based on what Nintendo has said/implied, I get the feeling that they DO have an official timeline and the reason they wanted to keep it a secret is that like the rest of us, they change it every time a new game comes out. Which I can actually live with.
Recently I've been reminded of Tenchi Muyo, which I only know a little about, but I think it's a good example of how in Japan, it's not unusual to have a completely new story with all the same characters and radically change things. There's one character in there who in one series is a demon that had been trapped in a statue until Tenchi accidentally let her out, and in another series she's an alien that crashes in his back yard. If Nintendo said, "these games are all one series, and this set is another series," I could probably live with that.

Btw Four Swords Adventures was made by Nintendo. It is Minish Cap, Four Swords and The Oracle games what were developed by a group owned by Capcom.