I am not sure how to remove the scratches other than buffing the paint but I do know you should never do the wax on/wax off thing on a motorcycle. Always apply and remove the wax in the same direction as the air flow would hit the panel you are working on. If you do the "in circles" thing you will end up with swirls. But I guess you already know that.
Use micro-fiber cloths, they really help not scratching. You probably have found out by know that the clear coat on the Wing is a lot softer than on cars.
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