I know on the Power Commander website, the model numbers on the unit itself is different for the 03-05. They only maps on the website for the '05 is graves slip-on/full, and euro bike - Leo Vince full exhaust. So, you will most likely have to take the bike to the shop for a custom map.
I am originally from PC. Maybe when I come down to visit we could hook up and go ride. On the power commander question, I wanted to know if the plugs are the same because then the only thing different would be the map #s and that isn't a big deal. I guess no one has put a pipe on their 05 yet? I think I am going with a Hindle anyway.