I've been pretty busy lately, and so, haven't been able to read as much as I'd like. This will cover the last several chapters. Please excuse it's length.
Dumbledore made a serious mistake in forcing Harry's hand. People don't like being manipulated, especially people like Harry, who have devoted their lives to a certain goal, only to have that all rendered moot in a flick of a wand.
Harry' discussion with Voldemort is a nice twist. Effectively: "If you leave me alone, I leave you alone."
His warning about the muggles is also a good idea. That seems to be one of the weak areas in the wizarding world's perceptions of the other 99 percent of the world's population.
It turns out you and I agree on Snape's character. Either Dumbledore is totally naive and truly believes Snape's 'remorse' or he has convinced himself that Snape is his pawn. There are far too many inconsistencies, in canon relating to Snape. His 'spying' is suspect at best.
He leaked information to Dumbledore, but how much of that information is truly valuable? How many of Voldy's plans were spoiled by his 'spying'? My guess is none.
In addition,, Snape's value as a spy would have been rendered worthless by Dumbledore's 'outing' him in a public venue, unless he was ordered to be an agent by Voldy.
I especially liked: "the 'greater good' clause in heaven."
I really feel for Hermione, but she was so set on breaking out of her 'bookish' persona, without taking into consideration her personality. Her attitudes are ingrained by her rearage, and trying to shed that persona will only lead to ulcers. On the other hand, her current attitudes have made her position in Gryffindor somewhat uncomfortable.
It seems Snape has discovered Harry's dark side. I think it's not so much that Harry is immoral, as he is Amoral. he does not actively hate Snape, but he sees him as an obstacle to be removed or neutralized.
Voldemort's introspection brings quite a few things to light. He seems to be less 'evil' than he is painted in canon. He is driven. A lot f Harry's cannon belief in Voldy's evil is fostered by both Dumbledore and his lot.
You have also done away with the horcrux tripe. The story was going allong so well, until book six when JKR stomped on the brakes and turned hard left. She brought Ginny-Sue out of the background and made her into 'SUPER-GINNY!', while reducing Hermione's IQ by about two hundred points and Having Harry think with his little head.
The investigation has cost Dumbledore a great deal of his political credit. While he cannot be ousted, his position is eroded. It shouldn't take much more to topple him.
I'd be willing to bet Dumbledore figured Harry would fall into Sirius' arms weeping in joy because his long lost godfather had come to rescue him from durance vile.
Instead, Harry's reaction was lukewarm at best. He was well reasoned, and cautious. He is definitely not a trusting soul. That can be laid at Dumbledore's door along with his other sins. He is, however, willing to work with Sirius.
As before, I eagerly await the next chapterr(s) of 'Elementary Calculations'.
Alorkin