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It took some time but I've figured it out. Sort of. I basically brute-forced things.
I downloaded and installed the Kobo Touch Extended plugin and configured it to match the one I was using before. (I then backed it up because I hope to never have to do that again.) I also downloaded two Kepub plugins that let me edit metadata, though I'm pretty sure I didn't need to.
I looked at Obok to see which books I had gotten from Kobo and checked all of them on the Kobo itself. About half had a working cover, which was way more than I expected. I wrote down the names for all of the ones without working covers and deleted them from the Kobo. Then I sent them again to the Kobo. They must have been converted to Kepubs during the transfer.
I also looked at a couple of categories where the collection name did not match the series name. I don't know how to coordinate these properly, so from now on every book I buy from the Kobo store will go through Obok, just so I can change the metadata properly. This means I'm converting from Kepub to Epub to Kepub again, but it seems to cause no damage. (I seriously doubt I will ever try to fix this. The absolute worst part about Calibre/Kobo, when I first got one, was getting the columns to work properly. Short of taking courses in computer programming I am leaving that alone!
Finally **one** book (that I deleted because of the cover issue) persistently gives me an "error in communicating with the device" message. It only happened once so it's not a big deal, but I can't fix it. I looked around for that error but it seems when other people get that error it affects every book. I might disable the Kobo Extended Touch plugin temporarily and use the older one and transfer that book to my Kobo again, although I suspect this will reintroduce the non-functioning cover error.
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