I have a 2009 model Honda unicorn motorcycle. It's very difficult to ride during rain or cold weather, because of missing. I asked service center but they did not do anything. I have changed the CDI, ignition coil and air filter but the problem persists.
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Check the spark plugs and plug wires. Maybe you've got a bad plug or a wire with a crack in the insulation that's letting in moisture.
Sounds like you're on the right track. Water/cold missing issues are usually ignition related. I've been down this road a number of times myself. It can be quite hard to pinpoint. Look for cracked ignition components that might be letting water in/support condensation.
Another (but somewhat remote possibility) is water in the fuel. Bad seal on the gas tank?