Just did it myself...
If you want to make the back look stock after pulling the double decker, you need to replace both the quarter panel interior trim piece and the two trim panel covers that secure the panel to the floor. The panel covers for double decker and non-decker panels are different shapes, which I discovered the hard way when making the conversion myself. After you make the switch, there will be a small gap in the carpeting in the back where the hinges to double decker used to be, but this is easily concealed if you have a carpet mat or cargoliner.
The part names, descriptions, and price from TRDparts4u.com:
Quarter panel - Interior trim - Cargo cover - Front w/o double deck
58401-35010-B0 or -E0, depending on color, B for stone, E for tan
$128.56
Quarter panel, Interior trim, Trim cover, W/o double deck
64721-35020-B0 or -E0
$12.78 each (you need to order 2)
Shipping cost me $18 from Texas to New Jersey. I was really happy with how helpful and quick Barbara King at TRDparts4u.com was in filling my order, so I recommend them without hesitation.
Not cheap, but I really needed the extra inch or two of vertical clearance for loading up my bicycles in the back of my truck.
BTW, if anyone wants to convert their non-double decker stone interior to double-decker, I'm selling all of the parts you need to convert the other way. Everything is in as new condition out of my '03.