Your question has too many components, so I'll take the first and go from there--the character who has the most inner conflict in Lord of the Flies seems to be Ralph. He looks most like a leader, which is why he gets elected to that position. The reality, though, is that Ralph has trouble collecting his thoughts and can't really function well without the help of Piggy. Ralph is the one who has always dreamt of being someplace without any adults; once he got it, he did his best but didn't really know what to do. His inner conflict shows itself physically: he bites his nails until they bleed, he hates his long hair hanging in his face, he is annoyed by his salt-encrusted clothes rubbing against his skin. These are simply pictures of his inner turmoil. He's aware his leadership is slipping on the outside; on the inside he is worried that he just can't think well any more. He is a physical being asked to do an intellectual job, and this is a source of conflict in Ralph nearly from the beginning.
Simon is in some conflict with his world and even directly with the evil of his world. Piggy is in a clear man vs. man conflict with nearly everyone on the island. Jack is in conflict with, well, I guess with the pigs and then with the other three main characters. The clearest inner conflict, to me, is Ralph's.
Ralph struggles with one of the most prominent internal conflicts in the novel. Primarily, his desire to establish and maintain order on the island causes him to question his leadership abilities quite frequently. As more and more of the boys gravitate toward Jack (and therefore display increasingly savage behavior), Ralph struggles to figure out what his best course of action should be. For example, he worries over whether to blow the conch and call an assembly, since the boys have been disregarding the sound of the shell. He fears that if he doesn't establish his leadership, Jack will gain more power. However, if he blows the conch and no one comes, he'll realize that he's completely lost his power. Also, Ralph's physical appearance--and his stress about it--indicates an internal conflict. He is obsessed with order, and is extremely bothered by his long hair and dirty fingernails. Obviously, this is representative of his desire for order, and the fact that as the novel progresses, it becomes increasingly difficult to expect and keep order.