I am now convinced that anything woodworking-wise can be fixed with a healthy gob of wood putty.
I attached the bookshelf base two nights ago. I did a pretty good job of measuring so the bookcase fit snugly into the base. There was a rather noticable gap however between the base and the bottom of the bookshelf in the center, as if the base bowed out a bit in the middle. My solution to this was to just fill the gap with wood putty and sand it down level to the bottom of the shelf. It shouldn't be noticable after painting, but I'm concerned about it cracking later.
Next time I think I'd build the base directly onto the bookshelf and then reinforce it afterward, rather then build the base seperatly from the shelf. I think that would be more appropriate for my XP style of building things.
Anyway, a little more putty and some backing material and we're ready to paint! Pictures when done.