Answers
1- Who said he was, Tobi?? That was probably a lie!!!!
2- He had 2 sharingans because he has a collection of them and can transplant eyes like contact lenses. (u can see the collection after sasuke beats danzo).
3- Books and Zetsu. Remember Zetsu records everything. Could have been left by Madara to carry on his wil.
4- If you see Kakashi on that period, he is already an adult almost. Also, since Obito has the 1st hokage cells in him, he could have advanced a lot in terms of techniques, power and reflex and kishi knows what else. Why you think he can use Kamui as he wishes ( Hint: Hokage cells.)
5- The controlling of the Mizukage could have been Danzo with shisui's eyes. I remember Danzo had a pony tail when he joined Hanzo to kill akatsuki members. So that explains the long hair. Or could have been Obito with Shisui's eye that Danzo loaned to him, or a genjutsu. Danzo also had something to do with the massacre. Remember when Tobi and Danzo met after the Hokage Summit and Tobi said: Long time no see, since the uchiha incident. Or something in that line.
6- Obito got Mangekyou Sharingan probably when he learned that Rin died.
Or he killed someone dear to him.
7- That is dissapointment setting in. Have u been let down by someone??? Yeah, that sucks and also when u all these dreams in ur head and aspirations and cant seem to bring them to reality, u kind of loose faith in everything, specially if u gave an eye to a friend that was supposed to take care of the woman u love, only to be let down. Promises unkept and so on. Pretty reasonable.
8- That one is easy. It's called trolling. Lmao! Could be Zetsu doing his thing, Zetsu could have been anywhere, he appears in the toilet, the soup, I mean, possibilities are endless. And he repaired him, gave him a new set of arms and legs and voila! Tobi came to life.
Let me know if I answered ur questions to ur satisfaction. And BTW, this chapter was genius.