Angle grinder is an awesome weapon when it comes to rebuilding a 'toon. Will cut rusty bolts and alum. with equal ease, and much easier to control than a saw. Harbor freight offers them at a price that makes them pay for themselves on this one project alone....
Re: the decking, that aluminum decking is not cheap, and to be structurally sound, "planks" should run from front to rear.
I looked at a ton of options prior to doing ours last year, including 5/4 planks (wood and composite), plastic sheeting, and diamond plate. I settled on plywood, for the reason Scott mentioned above. I won't be around when it needs to be replaced again.
I would caution against the "green" stuff too. The ply you're after is going to be 75-100 bucks a sheet by time you get it. I did find that I could get it a little cheaper if it was not shipped to a "residential" address. I had it shipped to a local trucking terminal and picked it up myself. Pretty painless way to save a few bucks....
Best of luck on your project! -Al