RE: Why did Daniel drink the Amnesia potion?
I think I've figured out a good reasoning for all this.
I question whether or not Alexander told Daniel to leave him for some reason when he was in the Inner Sanctum (More on that below*), then it was when Daniel was in the starting area that he decided that Alexander needed to be killed. Morally, he could not accept himself in letting such a man live. But he was scared... Maybe he was too scared to go back down.
Daniel knew that an attempt to even find his way back to Alex was completely futile in his current state, because he knew in his own mind that he would be killed, but AT THE SAME TIME, he couldn't live with himself to simply run from the Shadow and leave Alexander alone.--So, he devised a plan that would "Redeem [them] both". To write a letter to himself with the goal of giving his fresh-slated mind a false hope that he had good odds in killing Alexander. "He is old and weak, yours is young and strong! He will be no match for you.".. "Don't be afraid, Daniel!" He says to himself. The letter+potion idea was plainly a motivational boost to the new Daniel so that at least the former Daniel--who doesn't have the mental fortitude to act it out--knows that he's done all that he can to ensure Alex's death, and clear his conscience!
You might argue that if he wanted to create courage within his new mind, why would he mention the darkness at all? Well, Daniel needs to know that he can't fight back, or else he will, and he'll die--leaving Alex alive.
*As a side to this: I don't know about you guys, but when I was in the Morgue, and you hear Alexander say "What are you doing? I hear you breathing Daniel, do you hear me? Have you changed your mind?", I thought that he was communicating with me directly. "I hear you breathing...Have you changed your mind?" is very interesting and is what leads me to believe that Alex told him to buzz off, or even face the facts that the Shadow WILL catch up with him, and he should simply kill himself, Daniel agrees, leaves, realises his moral obligation, writes letter, potion, lamp, tinderboxes, run, hide, run, scream, hide, kill Alexander.