I'm pretty sure he would have died. Kabuto damaged Naruto's heart BECAUSE that was how he converted chakra from Kyuubi. Without that connection, Naruto was on his own, hence the sequence of things getting dark for Kyuubi.

However, any other injury short of getting his head chopped off could possibly be healed by Kyuubi.



As for toughest battle, I don't think it's fair to say that Kabuto was the toughest because he almost killed Naruto. Come on, the only other person who was actually trying to kill him was Gaara. And even Gaara was playing around with him.