Redfish Hunter
Gone Fishing
Process of elimination is obviously your only option but I keep thinking electrical. Did the bike gradually start running badly during the rain or did it start running badly all at once? I think that every piece of advice you have gotten so far has been good, and obviously I don't know the answer either. If the air filter got saturated with water would it gradually start choking the motor down or would it happen all at once? Same question for plugged hoses and cannisters. I thought about this some more, you would not even need to use a multimeter to check the obvious. You could let the bike run on the center stand and run water from the hose over various switches and sections of the bike and the more obvious electrical connectors until it started to run badly. Just some thoughts, I hope you find it no matter what.