It's a quite strange move to leave Harry standing at the end with his wand in his hand. I think that means Harry is still in a position to do transfiguration which is wordless.

I'm curious where Harry got the gun. Unless it's some kind of railgun, the bullets can't be safely transfigured. Perhaps he asked one of the professors to get it for him. While given guns to children is normally incredibly dangerous, it's par for the course in Hogwarts.

So we have the Alicorn princess resurrection and the power he knows not being Friendship, seeing as he could've discovered the flaw in his Horcrux 2.0 system only fitting one person by sharing it before...

Do not try to obtain Sstone yoursself. I forbid.

This was said by Quirrell in Parseltongue. If you can only tell the truth in Parseltongue, then Quirrell was really forbidding Harry from obtaining the stone himself.

If you send me a message with your email address, I'll make sure it gets to John. See you there!

Email sent, hopefully also received... (Apparently my last mail to John was put in spam.)

The Severing Charm wouldn't bring down a tree, so he'd started partially Transfiguring cross-sections through the wood.

Quirell saw that. Partial transfiguration is not the power the dark lord knows not.

Sorry if these questions are stupid, but with the long pauses betwen the chapters I find it difficult to remember what exactly happened.

1) What exactly is the puzzle we are trying to solve?

If I remember correctly, Eliezer wanted us to solve something before the story is finished. Which pretty much means now or never. I just don't know what exactly is the question. (Yeah, knowing the question is half of knowing the answer.) Who is Voldemort? Seems obvious that it's Quirrell. What should Harry do? What exactly is happening? What are the motivations of the main characters in the story? Who killed Narcissa Malfoy? Do we have a list of unanswered questions? How likely it is that answering them will provide a new view of the story, and will uncover some new possible strategy for Harry?

2) Does Dumbledore know or suspect that Quirrell = Voldemort?

I am not sure. At some moment it seems to me that yes: Dumbledore expects that Quirrell will cause some problems (e.g. when bringing a dementor). At some moments it seems to me that no: Dumbledore explains Harry that Voldemort should be killed without mercy at the first opportunity... and yet does nothing against Quirrell. I am specifically condused about the part (after Draco was attacked) when Dumbledore took the map and asked about "Tom Riddle". What did he know at that moment?

Also, I am disappointed that Dumbledore plays an idiot so successfully, that Harry actually treats him like an idiot. Thus two people who have best chance at defeating Voldermort, have trouble communicating.

Quirrell may have some blind sports about humans, but he is good at disrupting communication channels.

He thinks draco is much more suited to dealing with the politics, and that it's much less work to optimize draco's morals and hand power to him than to figure out how to navigate a political atmosphere for himself.

To put it crudely, harry plans to use draco as a puppet.

None of the theories suggested thus far explain the last part of the quote:

but then she died at the hands of a troll, and yet you lived.

The way I see it, Lucius could have been thinking one of two things (originally, before Hermione's death) to say that:

1. Killing Hermione would also kill Harrymort (e.g. Hermione is some quasi-Horcrux Lucius may have heard of).

2. Hermione would certainly survive anything that Harrymort survives (e.g. Hermione also has all the magic skill of Voldemort).