Unless you have done other things to the motor that make it need more air like increasing displacement, raising the rpm limit, or adding forced induction, the larger throttle body will just make fueling at part throttle more difficult to tune properly. Since Buell's FI is an Alpha-N system (looks at throttle position and rpm to determine fueling and ignition timing), a larger throttle body will flow more air at a given opening than a smaller one. 20% open on a 49mm throttle body will flow more than the same 20% open on a 45mm throttle body so the fuel and ignition values that correspond to a 20% opening would have to change accordingly. The 45mm throttle body provides plenty of flow for stock motors and even modified XB9 motors.
If you have the time to completely remap the bike with a larger throttle body, consider pulling the top end and doing some light port work to the heads instead. You will get a much larger gain from blending the factory ports than you will with the larger XB12 throttle body.
