I'm glad you asked:
I believe that the scene we saw at the end of Amazing Spider-Man #697 where Norman Osborn mysteriously escaped the hospital was not actually taking place at the same time as the events shown in the story but actually a flashforward taking place shortly after the events of Amazing Spider-Man #700. Consider that Julia Carpenter was in that very same hospital as Norman, and just because she's in a coma doesn't necessarily stop her from using her psychic powers. What I think could've happened is after Peter died at the end of Amazing Spider-Man #700, Julia was able to use her powers to grab a hold of Peter's astral body/soul and then placed it in the body of Norman Osborn--who if you recall in his last appearance in New Avengers went into a vegetative/catatonic state due to his brain being overloaded by the powers of the Super-Adaptoid. This would also explain why the guards who should've been guarding Norman weren't there, because Julia used her telepathy to make them leave, allowing for Peter in Norman's body to escape.
EDIT: Also, Superior Spider-Man #8 and #9 established that Ghost Peter wasn't actually the real Peter but Peter's memories that Doc Ock kept having gained self-awareness and thinking they were the real Peter.
As for the Goblin-Kids firebombing MJ's nightclub, notice the Green Goblin didn't actually order them to this; this was something they decided to do on their own initiative when they realized the spider-bot could no longer detect them. All he was doing was testing to see whether he could hack into the monitors and for them to see if it worked or not. I also speculate that, if the Green Goblin is indeed Peter, then he was also making a misguided attempt at trying to protect MJ from Doc Ock by shutting down the spider-bot, not realizing that the Goblin-Kids would use the opportunity to cause "mischief."
Dude, that's awesome. I love reading your posts in here. Thank you for explaining that to me.