One of the reasons I got my JKU was to haul my dog around (I had been using my SRT-4 with all the seats removed except the drivers seat, but I figured this was better) so I removed the rear seat and made a hinged 3/4" plywood floor. I made brackets that mount to the factory seat bolts, that the hinges mount to. There's no more gap in the floor like there was with the seats folded, and there's room under it for my entrenching tool, spax axe, etc.
I found a large cargo pet liner on Amazon https://www.amazon.com/gp/product/B01CWHBMZK/ref=oh_aui_detailpage_o06_s00?ie=UTF8&psc=1 that's great. Bottom is rubberized so it doesn't slip. Long enough to go all the way up the front seat backs, and has a zippered pass-through. Covers all the way to the back (and then some) and up both sides. I added snaps at the corners, and to the plywood, so it's super secure. Also added eyelets and use Velcro strap to hold the sides to the roll bars, and Velcro tape to the back gate.
This is awesome. Great build. I sleep in my Jeep some, but need the rear seats for my dog especially on long trips where he won't lay down. I didn't realize how easy it would be to remove the 40% and do what you did for storage underneath and a flat surface for the dog and gear.