Like many on here have said you have to raise the idle up, I raised mine to 1400 based off of others suggestions and it works great. The reason that the bike runs rough when cold is because it hasnt had time to set it's self in closed loop meaning the oxygen sensors havent heated up enough to be used so the computer puts itself in open loop. Basically open loop is set parameters in the computer to comand the fuel and ignition timing. Once the O2 sensors have heated up enough to become active it will go into closed loop where it will run based off of real numbers from the exhaust and that allows the computer to adjust and run smoother.
It is nothing new or anything to worry about, open loop will always run rougher than closed loop. Since the muffler is allowing more airflow this will cause the engine to stumble a bit at lower RPMs, just raising the RPMs will make it idle smooth. Refer to your owners manual for idle adjustments, it's very simple and will take you about 5 minuets if you have never done it before.
Good luck!