your exhaust smell could be a small exhaust leak from the rear exhaust manifold area. Most likely from a gasket. Once the exhaust manifold warms up it expands and does not have a sealing issue. That area is inches away from the fresh air duct. My 2000 vulcan has a leak in that area. I don't care about the smell, I hate the sound. It goes away after about 1 minute. Glad to hear your original issue is fixed. I would have liked to come accross an issue like that in my dealership days. I liked challenges.