I'm not sure but how about a little more info.
How long has this been going on?
When did it start acting up? mileage, before or after exhaust, before or after K & N filter.
Does it only happen off idle or does it sometimes stumble when you wack the throttle on the highway or other times?
Its been a while since I've been able to ride mine(it's a 2000 also) and I can't remember how mine acts off the line. If I remember correctly at really low speeds with the throttle just bearly open it does stumble a little. The reason I asked about the highway speeds is that is the way mine was acting and I found out that the cam chain was off by a tooth when the recall on the tensioner was done.
Others will post here soon I'm sure maybe someone else can help more. And if I haven't already said it, Welcome to the board