I coded this plugin in short for myself and my website alone. I came to realize that there wasn't any such plugin that does something like this.
This plugin allows you to add the conditional Login/Logout, and Register/My Profile links to any custom WordPress menu you've created. You can add them selectively, and/or to more than one menu if necessary. (Requires more code, which I won't provide -yet.)
I haven't coded an 'admin backend' for this plugin yet, it's simply the core functions as of now. I coded this for my own website http://webmasterguy.com in which I needed such a plugin.
To edit which menu it selects through the plugins IF statement, open 'Menu User Tools.php' and find this code:
** if($args->theme_location == 'top-menu') **
Change top-menu to the menu slug of the menu you would like to have Menu User Tools hook onto. You must have all the menus registered in your themes functions.php
You can easily have Menu User Tools hook onto all menus, simply by removing the above IF statement in the plugin file.
If you want more functionality out of this plugin you're going to have to code it yourself for now.