So, the solution? Make it a flat surface again so we can put up bookcases. How to do that? Tables. Tables that have short, medium, and long legs. Having a wife that's a fan of the mission style of furniture, and thinking that mission style furniture looks comparitively easy to build, we had our general design.
Having finished the tables previously, the only thing left to do was build the actual shelves. And as of today, there are now shelves in place atop those tables. The same sort of style and design cues used in the tables were used for the shelves, so they would look at least somewhat like a unified piece. Additionally, the lower trim of the shelves actually descends past the bottom of the lowermost shelf, to hide the joint between the tables and the shelves. The two pieces are not permanently attached, which means that in the future, if we move, we could leave the tables which are custom-fit to the space, but take the shelves and attach small leg stubs to the bottom, making them oh-so-versatile.
So, once again, without further ado, pictures of the allegedly properly built shelves!