AEM should sell replacements. It's just a K&N filter, so any other K&N that fits will work fine. If you want something better, you can get a K&N XStream filter. The top of the filter is also made of filtering media instead of a metal/plastic cap, increasing airflow. I believe hjkim483 is selling his brand new, so you could get it cheaper than what it costs in stores. If you wanna go a step further, you could PM EasyC and see if he can get you a brand new style of K&N filter, the same that's being used on the TPR intakes. It has the most surface area of any K&N filter of its size (inverted center w/ filtering media), AND has a built in venturi to accelerate air into the intake.
It's not necessary to try to keep the filter dry, since it will always get wet in the rain anyway. As long as you have your undercar and wheel well plastics still intact, you don't have to worry about hydrolocking. You could get a heatshield to help keep the filter clean, though, but they tend to make it harder to remove the filter in the tight space. Here's one for a good price: