You can do the "ultimate airbox mod" to give it a bit more air pretty easy, this keeps water out just as good as stock, if you do a search you will find lots of pics of this mod.
I remove the flappers actuator, stick a drift through the hole it leaves and hit it with a hammer, this removes the entire flapper in minutes which is way quicker and easier than what the guy who named it the ultimate airbox mod did.
You can also cut a hole in the airbox above the airfilter to give it more air, oddly this area is protected from water better than the stock opening, I have a 2 1/2 by 2 1/2 inch hole there on mine. I ride a lot of wet/muddy trails and get some water splashed onto the stock airbox opening but never get any near the hole above the filter.
I have a programmer and fmf pipe to go along with the extra air the motors getting, I never tried it without a programmer.
Some guys run with modded airboxes with otherwise stock bikes with no issues, I don't think you will hurt the motor as im not adding any extra fuel at wide open throttle with my programmer anyway.