As far as the counter seal goes, I used 2 strips of the weather seal (shown below) laid in side by side. After that I I laid a piece of kitchen "Saran" wrap over the gasket material and put a bead of silicon on top of the wrap, right over the top of the gasket. Next I set the hatch cover on the silicon and applied light pressure with a small bungee. This gave me a raised silicon bead around the inside of the hatch cover that conforms to any variations in the gasket material. My Guillemot stayed pretty dry when surfing, (the front hatch is submerged for almost the entire ride in.)

More picture here, but none of the silicon seal...

http://www.flickr.com/photos/tonyolsen/11423043/in/set-605979/lightbox/

Good luck!

Tony