As much as i enjoy crazy as sci-fi stuff in reality, that whole thing about the invisible ship is the prototypical conspiracy theory, there is just as much evidence to disprove it as there is to verify it.
Not to rain on your parade or anything...

But as for an explanation for Jacob, I don't think there really is one. To me, "Jacob" is some kind spiritual middleman between the island and whichever human is in charge of protecting it. Just a physical manifestation of the islands powers, for the purpose of commuicating its will. It was Jacob for Ben, its Christian for John. That doesn't explain why Claire was there though. Hopefully next week Sawyer and Miles make their way to the cabin...