Not sure if this was explained already, but for the links that come from sequels of games, are they the same link but just from the future, or are they completely different?
They're completely different! I am taking Nintendo's timeline and stretching it as far as it will go, so the events of each game, including the sequels, take place much further down the timeline. Each game has a new hero (or heroes), rather than continuations of the same hero's story.
The only exception to the timeline stretch is the oracle games. Those two happen congruently in the timeline, so the two heroes are doing their own thing in Holodrum and Labrynna at the same time as each other, and eventually meet prior to the start of this AU when they team up to fight Ganon at the end of their journeys.