Pondering LOST has lead me to a simple explanation of the relationship between this "light", space, time travel, whispers and the afterlife.
My ideas are best explained by a simple diagram:
The diagram contains the following:
http://img704.imageshack.us/f/94488729.png/
X, Y, Z - The dimensions of physical space.
T - The dimension of time
C - The dimension of consciousness
Light - The golden light under the cork.
The theory is simple. The island is the place where the veil between space, time and consciousness is at it's thinnest. The light is energy that, when quantized, can allow information to pass between these dimensions of measurement. This is why lost contained both manipulation of time and consciousness (foresight, the whispers, hugo seeing the dead). IT also explains Mother's reference "a little bit of this light is inside every man".
The "Flash-Sideways" are virtual reconstructions of physical space, allowing the consciousness of the characters to resolve their issues and come to terms with their deaths (re: Matt Fox's view on the Kimmel Special).
The light in the church is not a heaven like destination, Instead it is the ultimate end (which is why Desmond continually referred to it as leaving, Christian said "You're not going anywhere - you're moving on"), the characters (who have already lost their physical forms) are also giving up their consciousness and ceasing to exist altogether, becoming part of the light to be reused and recycled back into existence. Ben has not yet resolved his issues, he is going to have a chance at love, something he never had the chance for in life.
Michael is unable to resolve his issues, unable to come to terms with what he has done. He may at some point be able to move on but for now he is stuck. He is stuck in consciousness, just like the other "Flash-sideways", except it manifests differently for him. The whispers are dead minds seeping through the veil and into the island.
The reason Hurley can see Michael where the others can't is because he has a gift, he is able to feel the presence of Dimension C more potently than the other losties. Unlike the others who are only aware enough to hear the sounds, Hurley can also project them in physical from before his eyes, he can also reach them beyond the island veil, as Jack was also able to do under extreme emotion duress (when he saw Christian off-island). Miles gift is different, he connects not to consciousness like Hurley, but instead can find the imprint of a persons final moments in time if he is at the XYZ coordinates of the event.
Locke was also connected to time differently on the island, his ability to know the weather changes were a result of this phenomenon.
Eloise had a connection to time, one far more potent that either Miles or Locke. She could see the natural order of events (both in 3D space and C) and as such anything that happened out of order was considered a 'Violation'.
Walt projecting himself was another connection, but with physical space instead of time or consciousness like Hurley, Miles and Locke.
Time travel was achieved by manipulating the connection between XYZ and T. "Channeling the water and the light" into a different position. The island moving position physically was a similar shift in the connection (but only spatial).
Finally for now - The Cork: This I believe was there to control the flow of information between the dimensions. Some Pre-MiB civilisation (most likely Egyptians) dug too far and cracked the physical barrier. If the barrier was not closed then the flow of information between the dimensions would be uncontrollable, space, time and consciousness would not be able to take on any meaningful or coherent structure - This is supported by the physical destruction of the island upon removal of the cork.
A quick view on Smokey, from the 5D perspective.
The biggest question is why MiB and not Jack. I believe the answer is simple, Jack was alive, MiB was dead. After all, Jacob did kick an unconscious MiB down the gigantic underground waterfall, he likely cracked his head open at the bottom. Jack's 'soul'(consciousness) was still tied to his physical body, and MiBs was not. When jack was affected by the light, he was only displaced physically, for the Mib his body was physically displaced (to the same location as jack) but his consciousness suffered a different fate.
I believe that if MiB had died anywhere else at all he would have become one of the whispers, but the unique location of his death put him in a position where he could manifest in 3D space far more potently than the whispers.
That is all for now, please ask any questions at all that you might have, I'm hoping to expand this into an all-inclusive lost theory.