If it cut out when it started to rain then water is getting at th ignition somewhere so try to dry all the connection blocks out check the wiring for damage or water ingress. Look at the HT lead and cap and dry out and seal lead and possibly change plug cap if it looks suspect. Dont understand why there was water in the airbox but check dry out if water in there and dry filter or replace. It may pay to drain all the petrol out of the tank as there could be water in there and carbs injection systems do not like droplets of water. Once you get the ignition dried out get a spray can of ignition sealer and spray on exposed leads and tape if anything looks bodged. If ts got a injection system it probably doesnt have a choke so the ecu will adjust mixture from cold. Look up the cold start procedure some bikes need the throttle closed others you have to open slightly, what does the manual say on starting.
