If you would consider me to be a databank of Zelda knowledge, then I can confirm that the Skull Kid encountered in Twilight Princess is in fact, the Skull Kid encountered in Ocarina of Time and subsequently Majora's Mask. The reasons have been stated, and while he played a minor role in TP, it was conceptually of great importance.
Think about it..
The Skull Kid, a once major adversary of Link in the world parallel to Hyrule, having been scarred by the workings of Majora's Mask, now leads Link towards the Master Sword to the tune of Saria's Song, a song that helped Link, the Hero of Time, progress through his first adventure. Skull Kid in TP now reprises his role of a century past and simultaneously, that of the past Link's childhood friend, Saria, as both were denizens of the forest. It's only fitting that a character who once committed an almost catastrophic crime be punished by being tasked with leading the new hero to the sword of evil's bane, that which will help save Hyrule. He works inversely now of his past:
Skull Kid once tried to destroy Termina. Skull Kid now helps to save Hyrule. These lands are opposite, and so are the actions that he is partaking.
Now, speaking of Saria..
If we can account the theory that the Kokiri transformed into the Monkeys seen in TP (just as they transformed into the Koroks prior to WW), then the main female monkey may very well be Saria. We see that the Kokiri never age, and one so sacred as Saria would (if Kokiri are not immortal) have a prolonged lifespan, and hence, why the female monkey in TP has quite an affection for, and almost natural bond to Link. He is inclined to save her, and she is inclined to help him, just as the relationship between Link and Saria played out as in OoT.
So with that said, could the Kokiri, and specifically, Saria have actually been present in Twilight Princess as the forest dwellers living in The Deku Tree (Forest Temple)?