If it happens at all throttle positions I would suspect either something electrical or a vacuum leak. Maybe a plugged or improperly seated jet?
Be sure all of the little vacuum caps don't have any little micro cracks in them. A lof of us had that problem, easily fixed by just swapping them all out every year or two and cheap too.
It could possibly be a case of being way too rich or way too lean. Check plugs for this.
A simple check would be to replace the spark plugs with fresh ones. That may be the problem and at the least will give you a starting point from which to eliminate one thing at a time. Run it awhile (5-10 miles) with new plugs and pull them to see what color the center ceramic parts is about 1/2 way down. NOT at the tip, you should reference the color further down the core part.
Check that all your electrical connections are tight and even pull them all apart and give them a shot of electrical greeze for good measure. Maybe tighten the coil connections a bit too.
If it's electrical, that's a whole new ball of wax. There can be many things causing it and if it's intermittent it's even more difficult to diagnosis. Does it skip if you are sitting still and give it gas, or just while riding and under load?
Let me know what you find. Keep at it and you'll eliminate the pita stutter.
Here's a chart from another post that may be helpful too.
