Thanks for the info Gordon. I kind of figured, but I wasn't really sure. Now I know for sure I need to waterproof this thing.
Since I don't have all the parts yet, I don't know how big it will be.
It looks like MG Chemicals has some different potting compounds, including thermally conductive.
http://www.mgchemicals.com/products/potencap.html
I'm sure there are other places, (hopefully some local) but this definately gets me in the right direction. Thanks everyone.