Interesting question. Sasuke's whole side-quest does mess with us here... the easiest thing to do is to start our own story somewhere around there, but it all depends on what kind of characters we get.

Also yes, the idea is that we'll use the same roles as the series, but not as specific as that. So we'll have a jinchuuriki (biju either by choice or depending on what village we set our game in), the cool friend and the know-it-all. Of course, because of the golden rule of Naruto-teams one of them has to be a girl.