About Mangetsu, the Hydrification technique, while not classified as one in canon, seems a lot like a kekkei genkai of the Hozuki clan, in that it may be a change in his basic biology, like the Kaguya. If so it would take specific research to even figure out what is actually wrong, let alone cure it.
I've said my piece on the Cloud problem. And adding to Kisame, I think we may be able to just talk to him, assuming he still believes in our honesty. Just telling him we are not on a mission to kill him and that we want to talk should be enough. We could perhaps get him to tell us what's up with Akatsuki, explain why he thinks it was best to leave and what he hopes to achieve.
About Yuki, I'm the the guy who came up with that cheesy romantic scenario, so she might be my budding waifu, but really I don't see Shimaru being romantically driven. I think there should be a deep connection there though. If she was to be more forward though, what would Shimaru do? I think he could reciprocate, but would put duty before their relationship; no settling down to make baby Yamada-Kaguyas. I doubt Shimura could ever settle down, unless there was peace among the Five Nations. If Yuki wanted to I could imagine him being opposed to losing her as a swordsman for the time it would take to even birth the child, let alone raise it, and it's not like either of us have close family that we could entrust one to. We would have to find someone we wanted as a guardian and Oh God Why am I taking this so far
I'll think more about the Nindou, determination replenishment stuff and maybe post later.