Thank you for all of the suggestions.
However, now that I've figured out how to open Calibre to the library of choice by modifying the shortcuts, perhaps it's best just to stick with Calibre, despite some of the other minor things that bug me. It would certainly save me a lot of time and frustration. I've already managed to get a new library mostly set up how I like it and really it's just a matter of ignoring the "All Books" tab for virtual libraries. Maybe someday there will be a way to rename that.
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