Before we get too focused on the bearing, think about this..... The inner race of the bearing is what turns with the shaft. There are a lot of balls between the inner and outer races....the balls roll with an individual rpm much higher than the shaft, and lots of bearing balls would pass by a potential flat spot on either race for every rotation of the shaft.
If it was mine, I would drain the oil, drop the pan, get a strong light and crawl underneath. Have a pal turn the output shaft while you look and listen. You might have a small piece of debris jammed between a couple of gear teeth on the output shaft, for example. Hopefully you can see/feel/hear the exact issue and determine if it is something you can correct then and there (like something jammed between gear teeth), or whether you'll have to pull the engine and split the case.
Quote from Dave-and-his-550 Today at 03:34:32 pm:
Is the bearing on the riders side of the bike?
PS: Dave, which is the "riders side" of the bike? I personally throw a leg over each side, but I wear pants so I don't have to worry about a skirt blowing up in the wind.