It's all in your imagination
I'm going to have to agree with Bipper on this. I'm a huge fan of The Legend of Zelda series but when it comes down to it, I'm downright certain that a timeline of any sort was never actually planned. It is my belief (call it stupid if you like, you won't hurt my feelings) that every single story from the series is exactly what the title implies: a legend.
Think of this every time you play a Zelda game...
You're controlling a boy that is the main character of a story being told by some random person in Hyrule some time long after the actual events occured. To me, each game is a story about one boy that protected a princess and, over time, the story turned to legend and evolved into the many different variations of what might have happened during the one adventure long ago. Sure, some of them show clear signs that they are sequels/prequels to others but they could only be mere extensions of the storyteller's imagination trying to extend "what really happened".