OK ...I got interrupted during my earlier post by family demands B-)
I would not use bed liner....The primary benefits of it are impact resistance and sound deadening which is not needed here. Minimize any opportunity to have two surfaces that rust can collect between.
This is very similar to the repairs I made on my '78 Newell 14 years ago which still looks great.
The best solution is to cut out all rusted metal and weld in replacement pieces. (That is what I did) If welding is out of the question riveting would be a distant second choice. The no-weld solution:
If the floor is too thin to support the trays I would cut it out leaving a 1" flange around the perimeter. Once all cutting and finish grinding is done I would coat it with the Over-Rust products from Eastwood :
http://www.eastwood.com/specialty-co...solutions.html
Cut your new steel floor to a size that will drop in and be supported by the 1" flanges you left from the original floor on the 3 sides that are not rusted up the sidewall. Bend a flange on your new steel floor that will cover the rust creeping up that one side. I have a steel brake you can use if you need to. Once you are sure your replacement floor will fit properly prep and paint with Chassis-black paint (Eastwood) or better yet drop it off at your local body shop and have them hit it with a couple coats of a 2 stage paint. Coat the contact areas with "Henry 209 Elastomastic Sealant" available at Home Depot....You must avoid all possibility of moisture getting between the mating surfaces from above or below. If you want to use solid rivets I have a Rivet-set you can use. Otherwise steel "pop" rivets should work. Once the floor is in place a couple coats of Gray over-rust paint on the whole compartment should finish it. You could apply a coat of rubberized undercoating to the floor and up the sides 1" or so before setting the plywood in. I have some 3/8 plywood that is laminated on both sides with fiberglass. That is what I used on the walls and floor of my water compartments. It would work on your floor if you want a piece let me know.
If possible have the battery bracket painted with 2 stage paint as well.