1.) Danzou is a dead man walking for killing that toad. When Bunta, Kichi, et al find out they're going to f*** him up beyond repair. It's a blood feud now.
2.) I still think that Naruto could come back without the messenger frog. The messenger toad was going to physically transport back to toad mountain. If he's there, then there are no toads in Konoha. Nonetheless, they would be able to summon him back. I think there is a sub-class of toads (at the very least) that can summon themselves to a given location. When Jiraiya died, and they told Naruto, all the major toads were there but neither Jiraiya or Naruto summoned them.
Yeah, Naruto's secret jutsu he's practicing looks awesome. It's definitely using wind chakra to slice those trees we originally thought were mountains. Naruto is going to slice and dice someone's ass.
3.) Kakashi still has some options against the first Pein body he is fighting. It blocks ninjutsu and taijutsu, so he still has genjutsu and his sharingan. The second body will have different weaknesses too.