95 Honda Foreman 400- Running Issues – Misfire

I made the mistake of going through some water and realized I was missing some vent piping off the engine. Water was midway up the engine and stalled out and water made its way into the engine. Flushed the motor oil 3 to 4 times till all water was out. No water made into the intake. Now it will start up but has a constant misfire through all speeds and only runs while throttling it or choked all the way. I have cleaned the carb and replaced the CDI box under the front rack as well as the spark plug. Any ideas at this point before I take it somewhere? Maybe a bad coil or stator ect. Looking for some help on this. Thanks