How cold natured is your bike?
Have problems starting it up after its been sitting for awhile? especially in the colder weather? do you ride less often in the cold because it can take longer to warm up?
I know my Kat is notorius for being cold blooded..if I dont choke the hell out of it, she'll carry on like a banshee till the blood starts flowin. It's not near as bad now as it was b/4 I got the carbs cleaned out and new plugs put in. If I choke her really good, she starts right up now and stays running, but still a bit rough. just par for the course.
but it doesnt stop me from riding though, i'll deal with it!