Mick, as wet as it is over there, I can only assume you've decided to install some drain plugs. If you're hung up on the plywood idea, have you looked at marine-grade ply in the 6mm range? You're probably able to get Birch over there, too. Since that grows in northern climes, I'd think it would be better against the weather in its natural state.
My solution to the floor noise business was to go with the rigid framework under the floors, at 90-degree angles to the tunnel. I've attached some early skeleton photos of the jalopy for reference.
I'm also using some thick diamond plate aluminum, so there won't be any flex at all. Rattling maybe, but no flex. I'll be using the heaviest aluminum rivets I have to hold it down.
Since you're a darn good hammersmith and apparently not afraid of .025 or .030 welding wire, have you considered welding lats or longitudinals either under or over top of what you've already got? It's pretty easy to fill gaps from the box tubing to the high and low points you've created by quilting, and the whole works would be joined if you decide to powdercoat the chassis when you're finished.
Can you send me some shots of the underside of the car? One from the centerline of the beam and the other from underneath one of the sides?
I really like the monocoque thing you've got going there. Brilliant. Here is a little reading for you on several different types currently in use, including one by Porsche that lightens the whole works and may fit the bill for your twadong noise (under the next-to-bottom section, called "ULSAB Monocoque"). It's good info, IMHO, but the spelling and grammar are suspect. It HAD to have been written by a good engineer!
http://www.autozine.org/technical_school/chassis/tech_chassis.htm