Some unanswered questions.

[Kein]

Hmmm...

- Why does the Shadow leave Daniel alone in the 'revenge' ending?

Because the original Shadow's Orb now help by Alexander. That's why he didn't want him to come closer - because the Shadow will kill them both.

Don't even ask why the Agrippa's Orb Shadow didn't kill Agrippa or why it didn't start to haunt Daniel when he assembled Agrippa's Orb... Too many question, no answers ;P

What the hell was Alexander, anyway?

He is a man, a member of Black Crow sect (or whatever it's called, AFAIR, it was black crow) who participate in (black) magic or something. Explain a bit (may be he found a way to live longer, which, actually, was his curse, because his beloved died and he still lives )

Recall the flashback scene in the Chancel in which Daniel describes the place as "Orpheus descending into the Underworld", and Alexander gets suspicious of Daniel for a moment because of his intuition.

Alexander was scared a bit that Deniel guessed his intentions to open the way to underworld/other world to find his beloved. I guess it's just Alexander who think the other world is actually Hell/Paradise or something similar. I bet no one really knew it, but -- remember Agrippa's words in teh end? He said: "He is a good person, help him Weyer". Weyer! He died long ago, and when all souls go (usually) after a death? Right, underworld. So, the Alexander was right after all, I think.

Why was Daniel able to simply piece an Orb back together with some adhesive (twice), when evidently Alexander could never do so himself with his own broken Orb?

Hmm... there is an explanation, but it's a pure guess. May be Alexander had an ability to protect himself from an Orb's effect (strong willpower and mind), thus, he saw no nightmares, which, I believe, made Daniel so sensitive to Orb's nature. He got it known in some way and was able to restore because of that.
2nd time it was an ability already.

What was the significance of the rose petals (or whatever flower they were)?

Some kind of reference to real things, requires a lot of time to wikipedia/google/dig it.