Hello,
Since the code from the master.css file is being generated from our LESS-CSS files, you'll need to create a custom CSS file for any overrides or additions.
In the /templates/TEMPLATE_NAME/css/ directory create a file called TEMPLATE_NAME-custom.css.
Add the following code to that file:
.gf-menu-toggle { display: none !important; }
That should disable your mobile menu.
As for the second issue, try adding your changes to the custom CSS file as well.