I don't have my arms around this whole thing yet, but I think a lot of people are missing that time travel, or really space-time travel, is the key. The Casimir Effect is mentioned in the Orchid video. Theoretically, this real physics phenomenom can be used to stabilize a wormhole so you can go from one point in space-time to another and back. In order to really do this, you would need a huge amount of energy, like that which is in the Sun, or like that which is hidden in different pockets on the island.
Remember the "exit" from the Orchid station that was somewhere in the Tunisian desert (with a time shift as well)? Well, the exit for the Swan station is the jungle nearby (without a noticeable time shift or was it a couple days before those three reappeared?) and the exit for the "source" is those branches where MIB and Jack ended up (without a time shift? How close was the time of the Ajira taking off with the time of Jack sitting in the pool?). I suppose in all cases they were lucky the other end of the worm hole wasn't on Jupiter or in the middle of outer space.
In any case, I don't really know what is going on, but I do know that MIB and Jack did not float out of the source and to those branches: they appeared there just like Ben appeared in Tunisia and just like Eko, Desmond, and Locke appeared in the jungle after the Swan blew up.
The Souce itself is just like the Swan: some ancient people kept digging and digging and caused some incident and had to plug the hole. Thousands of years later, MIB's people were probing the same energy and managed to build some mechanism to use it (or since they all got killed, perhaps some later peoples finished the mechanism).
I think the smoke monster is directly related to this as well.
The nature of the smoke monster is still not very clear. However, its ability to replicate people seems very interesting and familiar. The only other time we saw something like that was when the bunny in the Orchid video outtake appeared with its future self. Perhaps something like that is happening with the smoke monster "possessions."
I think the smoke monster is something from modern times (Dharma times or maybe the future?) that was sent back to ancient times. Maybe it happened during the incident. Maybe its Phil's spirit (joke)?
If that happened, this thing has had thousands of years to possess people and acquire their thoughts and mannerisms and develop its own mythology and rules of operation. Also, related to the bunnies, maybe we never saw it in Dharma times because it knew it had to keep away from its "past" self just like the rabbits had to be kept apart.
I think there is something to this, but that's as far as I can get with it.