In setup_options.php you just need to modify $dbUserShema array so it fits your users table structure. Other changes need to be applied in bb_cookie.php (where you need to rewrite authorization functions).
Templates are not affected at all. In user_dataform.html you just should remove link to the password restoration, or replace it with your own, so miniBB should not handle any of the standard routines for your users table, like registration, profile update, password restoration etc.
Using 2 databases is obviously not the best idea...
Also if you have modified index.php - that means you already did destroy the core file. index.php is the main core file
! In manual
, we describe what is called core file and what is not and could be modified.http://www.minibb.com/forums/manual.html#upgrades