You have a very good theory. I disagree, however, that there is only one half of Kyuubi sealed in him. There would almost have to be the whole Kyuubi. The way I always took it was that the Kyuubi's good chakra consatantly mixes with naruto's own, which is part of the reason Naruto has such vast amounts of chakra. The Evil chakra is what is behind the death god seal in Naruto (the whole gate thing). The reason I think both halves are in Naruto is becuase if there was only half that would throw a wrentch in Peins plan. What use id only half a Kyuubi. Then they would have to spend time looking for the other half and that would be wierd. (and if it was in death god then there would be no sucess in Pein's plan becuase there's only half.)