I believe I know why Sayid is now "bad" or whatever and what was with the water in the pool. This is a very vague theory, but I believe some of it is right.
When they brought Ben into the temple as a boy, I believe we can assume that they did the same treatment to him as they did to Sayid. However when they did it to Ben the water was clear or white even. When Ben awoke slowly his loyalty to both Jacob and the others grew until he was completely devoted to the island.
When Jacob died and the MIB "took over" the island, the water immediately turned black and now everyone who is dipped inside will slowly grow loyal to the man in black.
I believe that a long time ago Richard arrived on the island on the Black Rock, he met both Jacob and MIB, there was some kind of incident and it caused all three of them to gain powers. Jacob and MIB were luckier, not only did they gain immortality but other powers as well. MIB can change his form to either black smoke or to the dearly departed and Jacob can persuade or make it so certain people are in certain places at certain times. MIB became a problem, so Jacob, Richard and a few of the others bound him to the cabin in the woods and surrounded it by ash to keep him inside.
If he were to ever escape bad things would happen. Since MIB could change forms no one was ever sure if they could trust each other, so Richard and Jacob invented a code as a form of trust, that could is "what lies in the Shadow of the Statue?". Much like "What did one snowman say to the other?".
At some point however MIB escaped the cabin, no one except Jacob knew, so he traveled off the island and informed Ilana that he needed help. He told her the code and knew he didn't have much time, MIB would be trying to kill him and needed protection.
Claire thought she saw her father but it was really MIB in disguise and he slowly planted the darkness in her and she became "evil" or whatever. He wants to kill all the castaways and make them part of his army.
What his ultimate goal or how he escaped the cabin (what cause the small break in the line ash) I don't know, but this is what I have so far.