What was the biggest puzzle piece that clicked into place, please.

One was that  Leah may have already been infected before the party, just some of her actions speak to that.  I also think she was fighting for her sanity just as she was in Proven Guilty when Harry saw her under treatment in ice.  Another is what a dupe Bianca was, and that Mavra and others played her like a harp.  Last but not least how Susan willingly blinded herself to what was really going on.  She covered the supernatural but I doubt that she fully accepted the reality of that world and thus chose to ignore Harry's warnings of the dangers and made that fateful step of stealing the invite to the party.

How so? Catch a new clue?

Yes, or things rather some things seem to fall into place..  That was last year and I started and wrote three very long topics about it.

Bwahahahahaha .... WAY too close to a happy ending.

And why shouldn't Harry have a happy ending?  If he is indeed the author of the files, I'd say he has his happy ending..  However "happy" is in the eye of the beholder...

Harry is now the Merlin, he lives on Eb's old homestead and is surrounded by his daughter and many grand kids and nieces and nephews... He now has the family and peace he always wanted...

I do not think Margaret could have saved Thomas from vampirism, the only cure we know is unpredictable an impossible to plan.

I don't think she could have either, that may have been one of the reasons she left him behind when she left Lord Raith.  For starters she may have felt that given his slim chance to beat the Hunger he was better off being raised with those who understand it far better than she ever could.  Secondly she may have felt if she had taken Thomas with her she'd had no chance with Malcolm..  Lastly but not least, Thomas might be her secret weapon for ultimate revenge against Lord Raith.  It may not be just because he was male that Lord Raith has tried to kill him all these years.

My main question with Cowl: Is he A) nemfected, B) working willing with Nemesis to achieve shared goals, or C) working with nemesis with the intent to later betray them and try to take more power/exploit the situation they have created for himself?

I'd say that he is working for the same side as Nemesis, evidence for that is he delivered the infected Knife at Bianca's party...   Is he after a huge chunk of power for himself?  That was answered in Dead Beat when he attempted and almost pulled off Death Hallow.  The same could be said for Mavra, who was also after Kemmler's book.  So yeah, in that light it is a give that either Cowl or Mavra could betray the power they are working for in the belief that they could ultimately replace them.. 

I have to agree that Harry spends a fair amount of time helping Marcone's interests. Harry sees Marcone as a necessary evil. But, Harry has stated that Marcone is, also, on Harry's to-do list.

Yeah, kind of like what Mab said about Uriel in Small Favor, they had a common interest on that particular day..