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The simple answer is that the built-in import utility is designed to import a pre-defined list of fields only, and will not import your custom fields even if those are added to the import file, and you will need to use the API to import those fields.
However, there are unsupported methods of importing this data directly to the database, or to add the custom fields as available options for importing. I can tell you more about these methods offline from the forum if you are interested.