Okay, I fixed the update issue.
I closed ComicBase and tried to update from Sidekick instead and I noticed that it started trying to read titles right away and didn't download the update first. Sure enough the updated failed again, but this time Sidekick provided me an error message that included a filename. I suspect the update got corrupted somehow so I deleted the temporary file and initiated another update and this time it worked.
Cover downloads seem to be working properly at the moment as well, so maybe I jumped the gun in opening this thread.