When I picked my car up I didn't realize it at the time but some dingus removed the tool storage altogether. Now, behind my seats, it just slopes upward. It's annoying because now the interior trim vinyls just stop and don't blend into each other. For the meantime I just sound deadened the whole area and will carpet it in the hopes of making it look normal.
To answer your question, I plan to just fab in some metal and square it off to make it look correct. I will then just cut holes via a template or just leave it, still unsure. I have seen on ebay someone selling just that section though, but since you already have the donor, go for it. It looks like you'd just cut it out at the seams and swap it over. Looking at my car, it doesn't look like there is much holding that section in so it might be a pretty quick swap.