Well, I had been getting water in my cargo area for some time now. It all pools in the cubby, anything left in there will get SOAKED!
Today I cut the rear section of the carpet out. I cut it in such a way that I can still put it back if I want and it won't be noticeable that it is cut.
I think I found the water's source of entry...

Now, I'm debating on lining the cargo area and being done with the carpet. My concern is, I want to keep the plastic panels on the sides... and ripping out the carpet and pads, I'd lose about an inch of height or so, leaving a large seem along the sides open to things falling back there. What else can be done in this area? Should I plywood the cargo area and line it? That could get my up to the line of the panels. I'd probably run some sort of weather stripping along the bottom line of the panels to act as a seal between the panel and plywood.
If I do put plywood, should I add a layer of padding between the wood and sheet metal of the truck to insulate from noise?