Make sure your engine baffles are in top shape. Look for black streaks where cooling air may be escaping between the cowl and the baffles. I spray painted my cowl inside with red primer in the areas where it contacts the baffles. Air leak areas will show up faster on the clean surface. Use high-temperature rtv to plug up the small areas and make sure the slits in the baffles properly seal where required.
A couple of people have made cowl flaps and report good results. Removing the fairing boot could possibly do the same thing, but I would opt for the cowl flaps first.