The Goron's claimed that the Spiritual Stones were gifts from the King of Hyrule to end the Great War which was prior to the Ocarina of Time.

As for the Kokiri being immortal, no I don't believe that, but I do believe that they are ageless children, unless they go out of the Kokiri Forest. At the end of the Ocarina of Time we see both Mido and Saria out of the Kokiri Forest, meaning that they should then no longer be ageless children of the forest.

As for how the sages become sages, I think it is destiny, much as how alot of things arise in Hyrule.