Advice needed for importing custom field data and database structure

Unlikely that you will need intermediary database, from your description this is likely to be easy enough with bit of PHP and WP APIs.

  1. Create WP-Cron task (if you need automated recurrent import).

  2. Read data from flat files, for example with fgetcsv().

  3. Use wp_insert_post() for creating posts and custom field functions to add your data. This was recently covered in detail in WP insert post PHP function and Custom Fields question.

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