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Ok here we go.
Jacob is now in Sayid.
For some reason that I have yet to determine, Jacob knew he had to die. That's why he let Ben kill him by acting like he didn't know who he was. He also knew that Sayid was going to die that's why he had him taken to the temple. The note to the Japanese dude supposedly said that Sayid needed to live but that was only so the Temple people wouldn't kill the Losties.
The water wasn't clear and it couldn't heal because Jacob was dead. So Jacob got the Losties safely to the temple and got his new body by tricking the Japanese dude. Obviously the Japanese guy doesn't know everything because he didn't know that Jacob was dead when the water wasn't clear.
Also that's why in the note it said that Sayid was extremely important.
Following up on the Jacob not knowing Ben thing, it's become clear that Jacob knows everything that happens on the island because he knew about Jin and the Frenchies at the temple walls.
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