@davidfor
So I have again redone everything, this time in accordance with your tips and requests. I'm outlining everything I've done as I'm doing it; hopefully that will also both help with understanding & reduce futher questions

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1. Factory Reset
2. Signed into Kobo account on ereader
3. Downloaded all my books over wifi (of course, as this was the first sync, it took a while but it was definitely not an unreasonable amount of time).
4. Saved the "KoboReader.conf" file for you at this point in time (post-sync). Not sure if you need it here, but I figured it couldn't hurt to have a clean reference point. I couldn't upload it here due to the file type, but it is in link I will PM you.
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Have you tried using the Kobo desktop application without using calibre? This is just to prove whether it is an issue with using the PC or specific to something calibre does. And that is because I can't think what calibre is doing that would trigger this problem.
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5. Synced reader to the Kobo Desktop App
6. Re-synced reader to Kobo over wifi. This worked just fine, so it doesn't look like it's a computer issue. Saved the "KoboReader.conf" file for you at this point in time.
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You can sideload books by simply copying them to the device. If you connect the device without calibre running, you can copy an epub to the device and see what happens afterwards. The books should be imported by the device. And it shouldn't affect the syncing.
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Wow, that was super obvious... I guess when you always do things the same way, you forget there's other options. Blonde moment!
7. Copied a few books directly onto ereader
8. Re-synced reader to Kobo over wifi. This worked just fine, so it doesn't look like it's a computer issue. Saved the "KoboReader.conf" file for you at this point in time.
9. Opened up Calibre in debug mode (figured it couldn't hurt; this is the only thing I did differently from the previous times using Calibre) and sent the books to the reader. Saved the debug file for you. While the books were importing into the ereader, it stalled at 67% for a very long time. Then it restarted to reader (probably about when it would've went to sleep normally). Last time I didn't notice that, but I do remember that after I finished a book and updated Calibre, it did go back to that importing content screen again after I ejected it, even though I hadn't added any new books. So I connected and synced back up to Calibre, ejected it, and it finished importing everything.
10. Tried to sync over wifi to my Kobo account, and lo and behold, I had no problems... which is good, but really frustrating after all this work! I wanted to get the error to find out was wrong

. I've connected and disconnected to Calibre a few times now, and then syncing to my account again immediately afterward, and it seems to be fine now. However, I will still keep all those files in case it suddenly stops again. Probably will as soon as I hit 'submit'

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Steps 4-8 (and 9 - Calibre Debug mode) were not things I had previously done, so maybe there was something in those steps that mitigated the issue? I don't know... maybe connecting to my computer using other things first was the key here? Would debug mode make any difference?
I'm almost curious enough to try it again without steps 5 & 7 just to see if goes back to the non-syncing issue, but not quite curious enough to actually do it. If it becomes an issue again, I'll give it a shot that way first to see.