I think K & N makes a small, flat filter that would fit in the air box lid. Most of those style of filters have built in lips so if the hole was cut smaller it would fit in tightly. I would think this would allow more air into the box but still be resistant to water. Thoughts?

 

I did something similiar that seems to work really well. I cut a hole about 3 by 4 inches in the airbox lid. I then cut a piece of wire mesh about 3/4 of an inch larger all the way around and laid it over the hole. Then i cut a piece of K&N foam (comes in sheets) the same size and layered it over the mesh. Finally, i cut a 3/4 inch wide ring from an old plastic barrel and riveted it over the layers to the airbox lid. The engine breathes better and the air filter stays cleaner than with no airbox lid. Tip- don't oil the foam on the above because it clogs really fast.

 

Contact Quad61@att.net He's selling a product that solves the problem. Mine works great.
Ask him for pre-filter pics. and a price.