I just mention this because I am not sure its a problem yet..
I ride every day to work and home last week was heavy rain most days..
What I notice was when I put the bike on the stand in the garage and switched of the motor that there was excessive amounts of steam rising form the Cat eliminator pipes, at first I thought the thing was on fire and smoking.
My point here is that I removed the right side panel which was directly above the rising steam and the Condensation on the ECU my PCv & AT unit and all the Connectors was a little alarming to say the least..
I removed the ECU connectors and PCv connectors immediatly and put lots of Dieletric Grease every where I could..
I will look for some way to shield the contents of the R/S panel to stop the condensation.
I don't know if this is related to your problems but I thought it was worth a mention.