On mine, I wedged a small square of sponge in the air box, (just beneath the air filter, where the gear lube vents in), just to catch any gear lube that blows through. Keeps it out of the air filter.
When I do my oil changes, I pull the sponge out and wash it out with dishwashing soap and warm water. Then I dry it with a blow dryer, and wedge it back in. Simple and crude, but it works.
I would go ahead and put a new air filter if I were you though. I'm at 4450 miles, and I just put my 3rd air filter in a couple of weeks ago.
But, I ride in all kinds of crappy weather, AND live next to 2 oil refineries, so mine sucks up an awful lot of crap in the air around here!
-Duke