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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.

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To diagnose cracked wires, its best to check it late at night when you can see the tiny sparks earthing against the engine case/frame. If the engine is dry use a small spray gun to lightly mist the wires, you should see faint arcs of electricity as they earth to the case/frame instead of arcing in the spark plug – Mauro Jun 10 '13 at 19:41

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?

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I had the same issue. That was because of water getting in carburetor .

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