Motorcycles sold in the United States are designed to meet stringent EPA emissions regulations, which result in engines making less power than they are capable of producing. This situation has been getting progressively worse for more than 20 years. Motorcycles sold in California since 1997 are even more restricted in their power output, due to the tighter emission limits imposed by the California Air Resources Board (CARB). The main mechanism by which emissions are being reduced is through extremely lean carburetion or fuel-injection mapping.
Consequently, the single most effective way to increase a motorcycle's performance without making expensive engine modifications is to rejet its carburetor(s) or remap the fuel curve of the injection system's engine control module (ECM). This can be done in conjunction with opening up the air intake and exhaust. Regardless of changes you may make to your intake and exhaust systems, unless you richen the fuel-air mixture to optimum for the temperature and altitude at which you are riding, don't expect to get much more power out of your engine.
Of course, those of us who live in Big Bear are once again blessed, this time by having the lean condition of a stock motorcycle engine offset by the naturally "fattening" effect of high altitude!