I've said to heck with it and am currently doing a factory restore.
I found I could get rid of the extra shelves that couldn't be deleted or renamed by renaming them in the Android app and then deleting them after a sync on the Aura showed the extras with the new name (of course who knows if they'll stay deleted
). Unfortunately that also caused two of the shelves to lose all of their content that weren't Kobo kePub's (lost all epub.kepub's and regular epub's). I just got fed up and reset the darn thing to factory (it's downloading updates now).
At this point, after reading over 50 books on the Aura, and I feel giving it a fair shake, I'm really hoping Amazon comes out with a Kindle that uses this larger screen (which I like a lot), because I'm tired of having to put up with all of Kobo's little quirks and problems. I just want to read my damn books, and in my experience Kindle's "just work" without any screwing around. Kobo does so much I like, but right now I'm quite frustrated.