Former S2R800 owner here. I had a PCIII and had pretty good success with it. Then again I had no choice at the time for a customer map because no one was doing that back in 2007/2008. The ECU mapping is preferred because it is less to go worn on the bike like the piggy back system the PCIII is.
Remapped ECU > PCIII > Stock ECU Map
I would recommend doing something to at least to take advantage of that exhaust. When you cut the air box lid open, get a flowing exhaust and remap its a whole different bike.