Allow direct access to files/folders within WordPress to replace wp-admin

Here is the scenario:

I would like to design a brand new wordpress admin for my clients (using WordPress autoload as the core to interact with WordPress). I have tried slightly modifying the css or even using javascript to manipulate DOMs, but it just seems very inefficent while I can just re-code a new page instead of manipulating existing page.

With that in mind, I created a new folder, say, custom_dashboard, and try to redirect the clients there whenever they visit /wp-admin. However, it always shows 404 NOT FOUND when I open mydomain.com/custom_dashboard/index.php or anything that is not /wp-admin.

My questions are:

1. What are some recommended approaches this problem? Is manipulating CSS & javascript via wp_enqueue_script and wp_enqueue_style the only possible way to recreate the new dashboard?
2. How do I allow direct access to a single folder/file within the WordPress installation?