You remember this wrong. Jack didn't estimate their time of death, he said they died a long time ago because their clothes would have taken at least 50 years before decomposing. More realistically, these skeletons should have been dust, but they cheated to have skeletons to show...

Classic misguiding comment by Jack, to distract attention from the real clue that these two were linked to the "origins" of the island's mystery, the Adam and Eve comment. They've laid quite a few clues about the antiquity of their mystery, right from the pilot - but it's not before the ruins of temples and the Egyptian statue they were more open about it, after misguiding us a while that Dharma might be behind all the mysteries on the Island.

This isn't a retcon by the writers, the "adam and eve" foreshadowing and the fact these skeletons had the ancient playing stones in a primitive pouch with them is pretty solid evidence they've known all along these two were Jacob's female predecessor and his brother, especially that they had Locke elaborate on the antiquity of the backgammon game (Sennet, Royal Game of Ur etc.) in another early scene.



This is most likely something like that: turning the Wheel not only displace the operator but also moves the island. The whole thing appears to be uncontrollable, and that's hardly the only example where trying to use the Island's "powers" has all sort of side effects. Desmond and the imploding hatch, incidents in Dharma days and so on.

There's all sort of "missing links" in the back story, but based on the comments (not really here) a lot of people who speak of "plot holes" and continuity errors (Jacob didn't feel like his contemporary self etc.) seems to forget there's 2000 years or so between Jacob becoming the guardian/MIB becoming Smokey and current events. 2000 years we know precious little about, except we can guess many people have been on the Island in the interim. It's unlikely it's only in the last 100 years or so (Black Rock, French expedition, Army folks, Dharma etc.) people have started coming. Of course, 2000 years is also more than enough time for Jacob and MIB to investigate the Island's mysteries and learn many, many things. Jacob probably failed with his candidates many time, and MIB probably tried all sort of strategies to get off the Island. At the end of ATS, there still wasn't a game, and Jacob didn't know/didn't create the rules. He also didn't learn about the Island being "a cork" from his predecessor. Their mission as his mother understood it (or was willing to share with Jacob) seems different from Jacob's explanation to Richard.

In the case of the Wheel, we at least know it's been used before (which might imply the Island in Jacob's time wasn't necessarily in the Pacific Ocean yet). Charlotte found a skeleton in the desert in French North Africa before going to the Island (most likely near the very same spot in Tunisia Ben was teleported to later). IRRC, she found a dharma trinquet on the body, which could explain how Ben learned about this. Maybe that person died of thirst/hunger, or maybe he was D.O.A.

Another thing not to forget about the Wheel is that MIB said many wells were dug up all over the island. Perhaps it's not always the same well they showed us previously and not only one has a wheel (at one point, the Egyptian statue was shown standing, and we haven't seen that at MIB's well's location, though that may have been a camera angle thing). We do know that it appears Dharma has built some its stations on top of those wells, because that's where the anomalies were. One well is below the orchid, another was below the hatch, and that one would have been the closest to the caves where Jacob and Mom lived (and it doesn't seem MIB's camp was so far from there). MIB's wells and wheel could well have the been the hatch's, not the Orchid's, and not the same wells Locke got burried under either (this one was standing centuries later, not razed like MIB's).