If SS is supposed to come before OoT then why is link "old link". Does the young link in OoT take place before skyward sword, if so why is he a Kokiri, I thought he was a skyloftian, or did he go back in time somehow.
It is not the same link. Almost all links in the different games are different Links. OOT Link was MM Link, LoZ Link was AoL Link, and WW Link was PH Link. Those are the only games that share common characters that I can think of. It explains this a little more in the ending of SS.
There is a significant period of time between SS and OoT. I guess you don't know this, but most of the Zelda games feature different Links. Nintendo has confirmed that many games have spans as wide as centuries between the games, though they have not said whether the different Link's are descendants or reincarnations of previous Links. Hope I cleared that up for you.