I read somewhere that placing a piece of foam between the skid plate and the engine would cut down this noise. But at the same time it seems that it could potentially block airflow thereby increasing heat which is not a good thing.
Since I had an old wetsuit that I don't use any more, I cut a piece of rubber from it to the shape of the inside of the skid plate and glued it in place with liquid nails. Anyhow, after the glue dried I bolted it back onto the bike. Since the rubber was only 3mm thick, it didn't cause any fit problems.
When I started my bike, I was blown away by how much less mechanical noise there was. The difference is amazing.
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