Then I would spray your choice of bedliner and then look for some heavy rubber mats for the floor. Think 1/2 to 3/4" fatigue mats, the kind you see in industrial workshops. Get a couple then cut them to shape to fit over the tranny hump and up the firewall. This will cut down on engine heat that will be pouring into the cabin once you remove the carpet and insulation.
FYI, most bedliners I have seen will hold mud and dirt too, but you will have the option to spray it out. Bedliner is also rough on fabric and skin. Keep that in mind when choosing one brand over the other. The Herculiner we used is really painful on bare feet and elbows (don't know about dog feet). We have not added any mats to the passenger areas, but we did throw down a big rubber mat in the back to keep from scuffing up duffle bags and gear. I got it at Northern tool for about $60 and it is about 1/4" thick with a vertical pattern on one side and smooth on the other. I think it was meant to throw in a pickup bed. We cut this one down to fit in her cargo area.
As for the roof, you may want to dynamat it or something similar that has a metal barrier. If you put any kind of foam insulation up there, the spray on bedliner will dissolve it.
We are considering insulating the GW with home insulation panels (blue or pink stuff) cut to shape, then having a marine grade vinyl headliner put in....but that is much farther down the road