Thought is was clutch but appeared to be electrics!

[Fazerider]

Are your flaps in the right position? That's not an impolite question, honest 

There are 2 flaps that drop down from below the tank, meant to keep spray away from the plugs. They should sit on top of hte front cam cover (so bent forwards) and not drop down into the plug "cavity". If they are dropping straight down, they can cause shorting probs.

That isn't the way Yamaha show them fitted.
I reckon the thinking is with what they refer to as the air guide plate on top of the cam cover intercepted rain will spray around the sides onto the HT leads. With it tucked down the plug cavity it'll be delivered below the top of the plug caps into the lower part of the plug well where it finds its way to the drain holes.