These are some cool storage options...http://offroadtrailtools.com/shop/index.php?l=product_detail&p=72http://offroadtrailtools.com/shop/index.php?l=product_detail&p=164http://www.dirtbagz.com/db_main_pages/db_main.htmhttp://www.dirtbagz.com/db_main_pages/db_main.htmhttp://www.dirtbagz.com/db_main_pages/db_main.htm
Here is my build thread for the deck. I literally winged it as I went along. I didn't have anything written down on paper for a plan. http://www.jkowners.com/forum/showthread.php?t=166161
For the building material, look at starboard or other similar poly marine materials. You work with regular woodworking tools, but it's a poly material. I've used it on several boat projects and have moved it over to some past jeep projects.
West marine, but it does need to be ordered. That's a bunch of change though, close to a grand. Dam that stuff has gone up in price.