Hi,

1) Please install a fresh copy of Kyoto, we have already fixed the issues on 1.1.0.

2) and 3)

First you need to install a plugin where you can insert JavaScript, the plugin name is Insert Headers and Footers

- https://wordpress.org/plugins/insert-headers-and-footers/

After installing, go to the settings and add the following javascript.

<script>
jQuery(function($) {
    $('body').on('click', function() {
        $('.m-nav-menu--mobile').removeClass('active');
    });
    $('.m-filters ul li a').on('click', function() {
        window.dispatchEvent(new Event('resize'));
    });
});
</script>

The first click is for the menu and the other one for the filters.

Feel free to ask for anything you need.

Kind Regards