You can run the Yoshimura pipe without having to add a fuel controller or remap the ECU. But, keep in mind that the bike will run more lean like this, but not to the point where you are going to damage the bike. To lessen how much more lean it will run, leave the baffle in. You will get optimal performance on a stock bike like this, and that information came straight from Yoshimura. I run no baffle, ever, at all.... I also have the Rapid Bike and it's properly tuned. I ran the exhaust with no baffles even before the RB came in, and it is a night and day difference in throttle response. The bike runs butter smooth through all ranges of the power band, at pretty much all throttle loads.
Adding the exhaust by itself was a big increase to the power, and you definitely feel it. Adding a controller gave me on average, a 2hp gain across the top and bottom, and nearly an extra 3hp in the midrange. I also saw the same gains in torque. This engine stock is rated at 68hp to the crank, and dyno'd 58hp to the wheels. Just the exhaust and controller with a fuel tune has it sitting right at 63hp now... so I have decreased the powerloss through the drivetrain by half. Not too shabby.