The Navigation logo size is defined by the height of the Menu items set in Customizer > Layout > Primary Navigation –> Menu item height. Let me know if that works, i can’t access the link – can you check the URL
In Customizer > Layout > Container – change the Content Layout to One Container.
The alternative to using the Navigation as the Header is to use the normal Header with your Logo and set the Primary Navigation to float right. This will provide more control over the logo and the nav.
For Google Analtyics the code goes in the WP_Head hook.
For Google Tag Manager you need to create two hooks – you add the first code to the WP_Head hook and the second code to the before_header hook and set the priority to 0.