Rewatching the show, I believe that the cliff cave was the Man in Black's lair, so to speak, where he recorded all the candidates names and numbers. The Lighthouse is Jacobs, and has his official list of Candidates. The reason that the caves and lighthouse numbers don't match in some cases is because the Man in Black wasn't positive about certain candidates numbers. They each respectively crossed off each name on their lists. Jacob may have also used the lighthouse to bring people to the island.