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Edit 2 files to remove the registration link
This is for your user.php page
/modules/system/templates/system_userform.html
Comment line 11 as below
<!-- <div><{$lang_notregister}><br /></div> -->
This is for the login block
/modules/system/templates/blocks/system_block_login.html
Comment line 14 as below
<!-- <a href="<{$xoops_url}>/register.php"><{$block.lang_registernow}></a> -->
If you have already disabled user registration in system>preferences then don't worry about someone going directly to your register.php page because they can't register.