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@gafitz,
The specific page you need to configure to suit importing your books into Calibre is Preferences - Adding Books
You will need to make sure that Read metadata from file contents rather than filename is unchecked and you will need to edit the Regular expression box to reflect your current file naming convention.
This won't change the filenames in the Calibre library but it should get the metadata imported correctly into the library in one hit.
{Edit:] Oops, too late, Serpentine got there first!
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