Jack up the rear and try to turn the wheels. If they turn it's not likely a brake problem. Take it out on a road trip while it's not raining. When you get back, do it again and feel the face of the rim. If that rim is hotter than the rest, then you have a problem. Check the bearings also. There are also some suspension things that could cause the clunking you are mentioning, but none that would cause smoking. Bearings or brakes are about it....Maybe some water splashed up on the exhaust?