I gutted the whole bed area and rebuilt it. I replaced the old pink fiberglass with a combination of 1/2" foil-faced polyiso foam boards, Roxul mineral wool batts (better thermal and acoustic insulator than fiberglass), and foil-faced flexible polyethylene foam. That flexible foam is great; I've also worked it in over the wheel wells in back. I plan to put that under the carpet in the cab eventually too. I got it from http://www.lobucrod.com/
Luckily, I had an apartment to live in. This was January in Massachusetts. During this process, I learned that the seal around the window frame was also bad. By then it was too cold to use caulk, so I covered the edges with tape until the spring.
I made new side panels of 1/4" hardwood ply, edged with black vinyl door edge trim from AutoZone. The headliner was (is) failing all on the whole van. For the bed, I turned the two ceiling panels upside down, and painted the side without glue a color I liked. I also used white foam underlayment to insulate the windows. That stuff is great because it let's light in, blocks heat transfer, gives privacy, and stops condensation. It's similar to this stuff:http://www.bestlaminate.com/standard-3m ... 7AodP0cAfA
In the spring, I took all the sliding windows off. I replaced all the plumbers-putty-like stuff they used originally to seal the window frames in with a nice thick bead of silicone caulking.