I really shouldn't be responding here since I might not have anything positive to add, but I notice two potential problems that have already been pointed out. The response by Coors when he asked if there were any mods was my first thought too. You are asking the aftermarket tuner to make adjustments for the air kit and exhaust. That's it's job, you say. Maybe I am just way behind the times but I can't get over the fact that Yamaha has spent considerable time and money designing and fine tuning this bike and, with the exception of race applications in which more performance is dictated, I see no need for performance mods. Yeah, that's not going to win me any points on this forum, but there is always a trade off when you try to extract more performance from a machine. Reliability ?? Having said all this, I hope your problem is moisture related as you stated that you washed your bike. Remember, bikes are not like cars in that they have much more mechanical and electrical components exposed and are venerable to water under pressure. I've learned things the hard way too. 
