I think the latest chapters just proved you right. Uchiha Madara's apparently still alive and is apparently Tobi of the Akatsuki, so you weren't just over-analyzing.
I never did realize just how dominant of a character Jiraiya could be, but after learning so much about his past, my view of him has changed drastically. I don't think Jiraiya will be killed by Pain, not because I don't think Pain's strong enogh (being the leader of the Akatsuki, Pain's an extremely formidable opponent), but rather, I just don't see how Kishimoto can kill off Jiraiya's character. There's still so much potential within his character.
Oh and for what it's worth, I don't think Pain's human. In chapter 371, he says "..I took out this body to kill an intruder.." - which indicates that he only "takes out" bodies to "take care" of business. Maybe that's just me over-analyzing it all, but I still don't think he's human.
Before I forget, does anyone know that the rin'negan can do? My curiosity's been stirred.