Have you looked at Hydroturf
? It's what they use on jet skis. I'm restoring an old aluminum v-hull and have really heard some great things about using this as a deck covering. From what I can tell, it's basically high-density EVA foam. I had them send me a few samples in the mail. It seems ideal for what I want to do. I'm planning to lay in a floor and then top it with this stuff.
Also, check out Tinboats.net. That's where I'm getting my crash course in boat modification.