I assume you are doing a "Save to disk" to get the book on the Glo. If so, go into the preferences for "Saving books to disk" and deselect "Save cover separately" and "Save metadata in OPF" file. Then, when you do the save to disk, it will only write the book file.
As to cleaning up the mess, I'd probably just delete everything and start again.
Of course, if you wait until tomorrow afternoon sometime (Sydney, Australia time), the calibre update will include a new driver that handles the Touch, Glo and Mini.
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