Similar probs here with 2 FJR's after a heavy (aka typical UK) rainfall.
Below relates to an 02 gen1 FJR1300
Got back to my workplace after a really heavy rainfall to find my bike would turn over but refused to start. Moved her inside and took a look
Findings: found that the rain (water lol) had followed the loom from the ignition to a block connecter underneath the fuel tank and had managed to soak the whole thing. on closer inspection, i found that this must have been happening for some time as the connector pins were somewhat corroded and in a pretty shite state.
Left the bike in work (after adjusting every security camera focussed on her) (dont trust any of them) and went off to source some replacements.
Following day I spent a good few hours replacing the dodgy pins.
next project was to find a way of diverting the rain from running down the loom and doing the same, I looked at everything i could to adapt for the greater need and finally came upon a neoprene disc that was about 3.5 inches dia. i trimmed a small hole half the dia of the loom and slid it over said loom and slotted it just underneath the tank where i siliconed it into place and with silicone, created a water runoff away from the conn block. I also used a tiny amount of silicone on each pin slot of each side of the conn block to seal it.
Every other day sees me out with the WD40, just in case,
My method has worked, I just hope by reading this and taking a preventative step it wont happen to you.
Oh, it may be classed as sacrelege (sp?) but my bike lives out in the open in the worst of weathers and is covered only for the worst of rainfall. My mentality says 'why cover it then get it wet riding in the worst of weathers'
Could never be a fair
weather rider, they miss out on soo much.
Hmmm, not bad for first official post eh??