For the books which give you a technical problem error message on the website, you have to use the Borders Desktop app (possibly you can use the Kobo Desktop app, someone else has been using it for their Borders account above) to search for each problem book title in the built-in store, and then pick "Download" when you see the free version.
This will automatically add a copy of the book to your Library on the website, and apparently the ePub links will show up a day later or so.
I'm afraid I can't help you with actually getting the books to display on your Kobo, as I don't have one myself. Hopefully someone else will.
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