I noticed the R running a little rough at lower RPMs at about 3,500 miles. It acted like it might be a mapping problem on the ECU as it would smoothe out after accelerating. Just to be safe I checked the air filter and was surprised to find an abundance of bugs, dirt and water damage to the fiber from a light 20 minute rain I had ridden through a few weeks earlier. A new filter cleared up the roughness. It's a direct and open passageway to the filter! You should check your filter if you notice it running rough and especially after riding in rain.