I know you said you cleaned the carb, but did you clean the passageways out in the carb body? A tiny piece of debris can clog those up and make it not run right. To me, it sounds like you have some debris still in the carb somewhere, but I could be wrong.
If you ride through a lot of water, I would put dielectric grease on all the plugs and connections and also around the spark plug boot. It's a good ideal to do that, anyway, even if you don't go through a lot of water. It'll help prevent problems at the wiring connections in the future.
Most 4-wheeler problems are caused by a loose nut connecting the handlebars and the seat!!
You only need two tools in life -- WD-40 and duct tape. If it doesn't move and should, use the WD-40. If it shouldn't move and does, use the duct tape.