I just quickly skimmed through the posts on here, so just a couple things I want to answer/point out for now. I'm working on a proper post that's a bit more LT-centric, I'll post that when it's done.
@ "I love you," vs. "Fondness."
This got brought up so I thought I'd comment on it too. The japanese text for this line was "suki," which is typically translated as I like you or I love you depending on the context. Fondness isn't inaccurate but it's a bit awkward sounding in English. Whether you prefer like or love is up to you but the implication is romantic nonetheless, thus Yuuki is basically thinking that her feelings for Zero are romantic. Fans can decide for themselves what the extent of her feelings are. ^^
Yuuki calling Kaname her brother/oniisama
There are three translations out now: one by senbyafanatic on livejournal, which is translated from the Chinese Raws. She translated this line as "My brother." The other two are the scanlation teams, S2Scans and White Lily Scans, and they both translated it as Kaname-onii-sama.
Zero Sacrificing Himself
I won't say it can't happen, but at the end of the day Zero is still an ex-human vampire and we don't know much about his abilities as a complete twin born to the hunters. The reason a pureblood is necessary for creating a new furnace is because as Kaname discovered, the only thing capable of destroying them is themselves, thus a pureblood sacrifice being necessary. As for turning a vampire into a human (I forget now if this one was actually mentioned on here or not, sorry!), I think this is also something beyond an ex-human vampires abilities.
Parent Metal
This was explained already on here, I just wanted to elaborate a bit. The furnace (or "mother metal" as it was called before) is where all anti-vampire weapons originated, thus it's like the "parent" of those weapons, their place of origin.
Isaya Setting up the Masquerade
There's possibly more to it, but I think that Isaya just wanted to stop being a spectator and actually do something for a change, like Kaien did. Possibly this is connected with the "50 years of memories," that he gained from his servant when he drank her blood, after he first woke up from his slumber. It seems like Haruka and Juuri were dear friends of his, though, and I believe it's because their children are involved in the current conflict and technically on opposite sides that he wanted to do something to perhaps honour that friendship. Maybe he was just hoping Kaname would give some kind of meaning to Isaya's existence, or end it.
As for the Masquerade Ball itself, it was somewhat random, but apart from the purposes it served in the plot I think Hino just threw it in to parallel the arc one dance (which even got an honourable mention in this chapter). She seems fond of the parallels between the two arcs, or characters.
Yuuki Erasing Zero's Memories
First of all, I'm fairly certain that Yuuki was successfully able to erase Zero's memories, since we had Zero's thought (while Yuuki was drinking his blood) that "something within him" was disappearing. And on that page, we see his memories of Yuuki. After she subdues him with her bracelet, we see Zero's thoughts again and he thinks that his memories of her are.... ['disappearing' I assume but it's not actually specified]
We have to also remember that this isn't just about Yuuki trying to ease his suffering; Zero hasn't been letting her out of his sight, and it's probably because he noticed something was up (chapter 86 he comments on how he doesn't know what's gotten into her). She tried to leave the Academy without telling him, but he seemed to know anyway and was waiting for her. She tried to convince him to stay because of his duties (and Zero is a dutiful person) and he chose to leave with her anyway. She gave him that speech about how she couldn't live with him and belonged to someone else, and he chose to walk into her house and force her to confront her own feelings. Yuuki knows that Zero wouldn't approve of this plan, which is why she never told him about it until she was erasing his memories of her existence. She also knows that he'd try to save her and he'd never forgive himself if he failed. So, from this perspective, Yuuki's actions make sense.
Zero will definitely remember Yuuki. Not only do we have an example of this in the first arc, when Yuuki remembered about Zero confronting Maria/Shizuka, but we have an example in this arc as well when the class president Kageyama remembered who Ruka was despite his memories being erased - and Ruka was someone he had a crush on throughout the first arc. Since in this case, Ruka's entire existence seemed to be erased from his mind, it's the best example we have of this happening in the manga and it's probably why Hino randomly included that scene at all.
Shiki & Rima on Kaname's Side
I don't think they're on Kaname's side so much as Takuma's. They were following him to the Association before when he went with Sara, and he's now back by Kaname's side. I think this time, they want to stick close to him. He seems to be a very dear friend to both Shiki and Rima, so they may want to protect him from doing anything foolish or even from getting too involved in Kaname's plans. I kind of see it being like Ruka and Kain - Ruka didn't agree with what Kaname was doing, but she cared for him and wanted to look out for him. Kain especially didn't agree with Kaname, but he wanted to look out for Ruka and protect her.