This is what I did following ciuser's guideline but with some changes:
Do a clean install of Codeigniter. Set up config.php, database.php etc.
Install Modular Extension:
Move third_party/MX to CI/application/third_party.
Move core/MY_Loader.php and core/MY_Router.php to CI/application/core.
Install Ion Auth:
Move the following Ion Auth folders to CI/application/modules/auth folder: config, controllers, language, libraries, models.
Move the files under Ion Auth/views folder to CI/application/modules/auth/views. (Without one extra layer of auth
as in Ion Auth.)
Run Ion Auth sql in database.