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So I tried connecting to an older Kobo Glo (same version of firmware as Aura), same USB cable, same computer, same Calibre, and was able to load 700 books with no errors. Series info was good for all of the books.
I then re-connected the Aura and went into the Device - Configure This Device settings and de-selected everything but epub (pdf, txt, and a few others were selected), and success! I was able to load over 700 books with no errors, and the Series info is there.
Not sure why having those other formats selected were an issue, as all of the books in Calibre are epub, but I'm happy to get this working properly.
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