If you're using numeric ID's, why not use the database's autonumber feature?
You can query the autonumber ID after performing the insert using SELECT LAST_INSERT_ID() (assuming MySQL)

What I'm missing in your question is how the events relate to the articles (which is quite important in determining how to fill the article_event_index-table).
Where does the content of variables @url_prepare, @html_ pages_files_extended, @output_concord_files_prepare, @sys_time_prepare come from?

You will probably need to insert everything in one go:

Loop through files-to-be-processed {
  insert article
  fetch article_ID
  loop through events {
    insert event
    fetch event_ID
    insert (article_ID, event_ID)
  }
}
[download]

Also, to avoid sql injection and use good practice, try this to insert:

my $sth_insert_article = $dbh->prepare( qq(INSERT INTO article (url, h
+tml_extr_text, concord_file, sys_time) VALUES (?, ?, ?, ?))) or die "
+Unable to prepare insert statement: " . $dbh->errstr;
foreach my $article_index (0 .. @output_concord_files_prepare) {
    my $records_inserted = $sth_insert_article->execute($url_prepare[$
+article_index], $html_pages_files_extended[$article_index], $output_c
+oncord_files_prepare[$article_index], $sys_time_prepare[$article_inde
+x]);
    if ($records_inserted != 1) {
        die "Error inserting records, only [$records_inserted] got ins
+erted: " . $sth->insert_article->errstr;
    }
}
[download]

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