did you spray the handlebar and ignition switches too?
when riding in rain at any speed, the majority of the water is going to come straight on almost level with the ground, but a good deal of it is also going to be thrown up and forward by the tires, is anything in position that the tire can throw water to a sensitive area?
not sure what breather you have, but my old 75 would pull enough water into the breather off the back tire or around the engine to choke and stutter, always thought it was spark, but noticed water dripping from the screw in the bottom of the airbox after a rain, pulled it off and there was quite a bit of water in it. Drilled a couple drain holes in the bottom and didn't have problems afterwards.
ken.