This is set at the beginning of the shippuden - as in, your characters (canon) will have to look as they did in the Shippuden. This also means Sasuke is still with pedo Oro, Naruto just returned from training with Pervy Sage, etc etc.
Better yet, the Akatsuki hasn't been near eliminated yet. We won't be allowing too many people join Akatsuki, so take the spots while you can.