K&N makes a filter that fits the stock Hamcan. Its very good and has sleeves so that screws cannot get sucked in. Its p/n HD-8834, around $50. I have been using mine with 20000 trouble free miles.

 

I have never ran just the K&N kit on my bike, the first thing I wanted to get rid of was the ham can, I just couldn't find a comfortable position for my leg that didn't leave it pressed up against it, this would be the kit I would go with if I wanted to keep the stock cover. I had looked at the K&N kit and knew where to get the info figured I could help you out. I love the Heavy Breather like creekhed1 and only worry about getting caught in a heavy down pour.