Some unanswered questions.

[Klarden]

Alexander may have became too vain and thought himself to be something else than a simple human being. It doesn't mean he actually was. The diary is written from his point of view

Open the super secret rar, there's Herbert's diary that never made it into the game.

Rose petals - part of the amnesia portion, apparently. May be a subconscious way of Daniel showing himself where to go.

Whatever the connection of Daniel to the Orb is, i didn't really get it. Maybe Orb sometimes "felt" that someone was "ready" for it and gave in.

We actually don't know if the shadow left him alone. Remember, that we see it from his point of view. Maybe he actually died, but dreamt of being left alone. If true, maybe Shadow felt that Alexander is a more important target. Or maybe shadow did leave him alone for some time - we don't know what happened to Daniel after he left the castle.

Actually, dead bodies appear/disappear in the game several times. Sometimes it's a sanity-dependent thing, sometimes not. Nothing in the game is what it seems, it might've been there before, filtered out by Daniel's brain. Or it never was there at all.

Lanterns are a reference or a connection to Penumbra series. They contain memories and experience of people who touch it.