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To change layout on Registration page you need edit the file et-registration.php in wp-content/themes/idstore directory.
To modify Cart and Checkout pages you need edit the files in wp-content/themes/idstore/woocommerce/cart and wp-content/themes/idstore/woocommerce/checkout directories.
We recommend you to make changes in a child theme.
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Is you host blocking some IPs or there is some restriction?
To fix the issue with pagination you need edit the file idstore/woocommerce/loop/pagination.php and replace the code 'base' => esc_url( str_replace( 999999999, '%#%', remove_query_arg( 'add-to-cart', htmlspecialchars_decode( get_pagenum_link( 999999999 ) ) ) ) ),
with this one: 'base' => esc_url_raw( str_replace( 999999999, '%#%', remove_query_arg( 'add-to-cart', get_pagenum_link( 999999999, false ) ) ) ),
Could you please show a screenshot what you want to achieve concerning your 3rd question?