Cory make sure you are getting power to the coils, also check if you are getting a spark at both plugs. It does not sound like the CDI if it only does it in the rain. Definately sounds like an electrical problem. If it is one plug, swop over the lead and coil connections and see if it does it then, no need to undo the coils, just take a note on which wire goes where. But don't forget to swop the lead over...
As Ben has said above apply dieelectric grease or vaseline to the electrical connections..
