Wrong activation/confirmation link in email

I've created a custom login page login.php inside the root. (e.g.: http://www.example.com/login.php)

/*
    LOGIN PAGE.
*/

// Login URL.
function custom_login_url($login_url, $redirect, $force_reauth ) {
    $login_url = home_url( 'login.php', 'login' );
    if ( ! empty( $redirect ) ) {
        $login_url = add_query_arg( 'redirect_to', urlencode( $redirect ), $login_url );
    }
    if ( $force_reauth ) {
        $login_url = add_query_arg( 'reauth', '1', $login_url );
    }
    return $login_url;
}

// Lostpassword URL.
function custom_lostpassword_url( $lostpassword_url, $redirect = '') {
    $args = array(
        'action' = 'lostpassword',
    );
    if ( ! empty( $redirect ) ) {
        $args['redirect_to'] = urlencode( $redirect );
    }
    if ( is_multisite() ) {
        $blog_details  = get_blog_details();
        $wp_login_path = $blog_details-path . 'login.php';
    } else {
        $wp_login_path = 'login.php';
    }
    $lostpassword_url = add_query_arg( $args, network_home_url( $wp_login_path, 'login' ) );
    return $lostpassword_url;
}
add_filter( 'lostpassword_url', 'custom_lostpassword_url', 20);

// Registration URL.
function custom_registration_url() {
    return home_url( 'login.php' . '?action=register', 'login' );
}

// Custom redirect admin locations.
function custom_redirect_admin_locations() {
    global $wp_rewrite;
    if ( ! ( is_404()  $wp_rewrite-using_permalinks() ) ) {
        return;
    }
    $admins = array(
        home_url( 'admin', 'relative' ),
    );
    if ( in_array( untrailingslashit( $_SERVER['REQUEST_URI'] ), $admins, true ) ) {
        wp_redirect( admin_url() );
        // wp_redirect( home_url( ADASTRA_ADMIN_PAGE) );
        exit;
    }
    $logins = array(
        home_url( 'login', 'relative' ),
    );
    if ( in_array( untrailingslashit( $_SERVER['REQUEST_URI'] ), $logins, true ) ) {
        wp_redirect( wp_login_url() );
        exit;
    }
}

// Custom Logout URL.
function custom_logout_url($logout_url, $redirect = '') {
    $args = array();
    if ( ! empty( $redirect ) ) {
        $args['redirect_to'] = urlencode( $redirect );
    }
    $logout_url = add_query_arg( $args, home_url( 'login.php' . '?action=logout', 'login' ) );
    $logout_url = wp_nonce_url( $logout_url, 'log-out' );
    return $logout_url ;
}

function custom_set_login_url() {
    add_filter( 'login_url', 'custom_login_url', 10, 3 );
    add_filter( 'logout_url', 'custom_logout_url', 15, 2 );
    add_filter( 'register_url', 'custom_registration_url', 30 );
    remove_action( 'template_redirect', 'wp_redirect_admin_locations', 1000 );
    add_action( 'template_redirect', 'custom_redirect_admin_locations', 1100 );
}
add_action('init', 'custom_set_login_url', 9999);

Now, all the URLs are working fine BUT everytime there's a new user registers or forgots password he receives an email with two links:

1. the confirmation link leading to the wrong (aka default) login page:

http://www.example.com/wp-login.php?action=rpkey=rMrHUdWY1NC1eDdHAc4elogin=averagejoe

2. A link to the correct login page:

http://www.example.com/login.php

How is it possible that the system doen't uses the custom URL I gave it, I need to have just the confrmation/activation link leading to the custom login page, like:

http://www.example.com/login.php?action=rpkey=rMrHUdWY1NC1eDdHAc4elogin=averagejoe

and not using a plugin.

Can someone help me?

Thanks.