It would be really good idea to add a PCIII when you do the air box mod, that goes for any bike that you do the modification to that is fi.
Once the bike is getting more air, it obviously is going to make it run more lean (plus, most bikes come lean from the factory) so it's definitely wise to get a PCIII to compensate for it, have it running as well as it can and correctly (ie; no stumbling, lean surges etc) for that matter. A lot of people will say the bike's computer will adjust for it somewhat in time, but in reality, by no means is it ever going to get the full benifit out of the modification and have the fuel to air ratio on par without a fuel tuner and a good map.
There are a lot of custom maps out there for different applications that you can simply download to your PC if you're not planning on getting a custom dyno tuned map. You can find these on forums specifc to the bike, PowerCommander's own website and aftermarket exhaust system websites.