I have just put a twobro's exhaust on mine and I'm noticing some rough idling when I first start the engine. It seems to fade out as the engine warms up.
I took my bike to the local yamaha dealer to have the shop guys there listen to it. Of course, the engine was a little warmed up when...
Let me know the out come b/c I'm having the exact same prob. and I just had a load test on the battery and it came back good. I think the cooling fan is whats pulling my battery down, even though it shouldn't.