Ed,
I usually store my rods in the A hatch(the beauty of that hatch is you can store any rod you want in there as long as its not as long as the kayak! You probly wont have to worry too much about getting your rods dunked but storing my rods in the hatch also helps me secure the rods on the ride home. My plastics I store in a dry bag, I think the SD sailing center sells those but I think you can find them at any sport chalet. The navigator performes well in the surf, I have punched through some 3-4ft waves without flipping. I haven't launched in formidable surf in almost a year so I have to get back in shape too. Good Luck, I'm planning on taking my kayak to Laguna very soon.
Tommy