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  1. I’ve found the answer here:
    Customizing wp-activate.php

    It’s a bit of a workaround really, but it works pretty well.

    Step 1
    Create a new page called ‘activate’

    Step 2
    Create a new template called ‘template-activate.php’ and add the following code:

    **Template (template-activate.php)**
<?php
/**
 * Template Name: Activation
 *
 */

/**
 * Confirms that the activation key that is sent in an email after a user signs
 * up for a new blog matches the key for that user and then displays confirmation.
 *
 * @package WordPress
 */

if ( !is_multisite() OR (empty($_GET['key']) && empty($_POST['key'])) ) {
    wp_redirect( site_url( '/wp-login.php?action=register' ) );
    die();
}

if ( is_object( $wp_object_cache ) )
    $wp_object_cache->cache_enabled = false;

// Fix for page title
$wp_query->is_404 = false;

/**
 * Fires before the Site Activation page is loaded.
 *
 * @since 3.0
 */
do_action( 'activate_header' );

/**
 * Adds an action hook specific to this page that fires on wp_head
 *
 * @since MU
 */
function do_activate_header() {
    /**
     * Fires before the Site Activation page is loaded, but on the wp_head action.
     *
     * @since 3.0
     */
    do_action( 'activate_wp_head' );
}
add_action( 'wp_head', 'do_activate_header' );

get_header();

//theme specific (CoWorker)
get_template_part( 'include/content', 'head' );
?>

<?php
        $key = !empty($_GET['key']) ? $_GET['key'] : $_POST['key'];
        $result = wpmu_activate_signup($key);
      $siteurl = site_url();
      $lostpassword = $siteurl.'/lostpassword';
        if ( is_wp_error($result) ) {
            if ( 'already_active' == $result->get_error_code() || 'blog_taken' == $result->get_error_code() ) {
                $signup = $result->get_error_data();
                ?>
                <h2><?php _e('Your account is now active!'); ?></h2>
                <?php
                echo '<p class="lead-in">';
                if ( $signup->domain . $signup->path == '' ) {
                    printf( __('You may now <a href="%1$s">log in</a> to the site using your chosen username of <strong>&#8220;%2$s&#8221;</strong>.</p><p>Please check your email inbox at <strong>%3$s</strong> for your password and login instructions.</p></p>If you do not receive an email, please check your junk or spam folder. If you still do not receive an email within an hour, you can <a href="%4$s">reset your password</a>.</p>'), $siteurl.'/login', $signup->user_login, $signup->user_email, $lostpassword );
                } else {
                    printf( __('Your site at <a href="%1$s">%2$s</a> is active. You may now log in to your site using your chosen username of <strong>&#8220;%3$s&#8221;</strong>.</p><p>Please check your email inbox at %4$s for your password and login instructions. If you do not receive an email, please check your junk or spam folder. If you still do not receive an email within an hour, you can <a href="%5$s">reset your password</a>.'), 'http://' . $signup->domain, $signup->domain, $signup->user_login, $signup->user_email, $lostpassword );
                }
                echo '</p>';
            } else {
                ?>
                <h2><?php _e('An error occurred during the activation'); ?></h2>
                <?php
                echo '<p>'.$result->get_error_message().'</p>';
            }
        } else {
            extract($result);
            $url = get_blogaddress_by_id( (int) $blog_id);
            $user = get_userdata( (int) $user_id);
         $username = $user->user_login;
         $useremail = $user->user_email;
            ?>
            <h2><?php _e('Your account is now active!'); ?></h2>

            <div id="signup-welcome">
              <p class="view"><?php printf( __('You may now <a href="%1$s">log in</a> to the site using your chosen username of <strong>&#8220;%2$s&#8221;</strong>.</p><p>Please check your email inbox at <strong>%3$s</strong> for your password and login instructions.</p></p>If you do not receive an email, please check your junk or spam folder. If you still do not receive an email within an hour, you can <a href="%4$s">reset your password</a>.</p>'), $siteurl.'/login', $username, $useremail, $lostpassword ); ?></p>
         </div>
            <?php
        }
    ?>

<script type="text/javascript">
    var key_input = document.getElementById('key');
    key_input && key_input.focus();
</script>

<?php
//theme specific (CoWorker)
get_template_part( 'include/content', 'foot' ); 

get_footer();
?>

    Step 3
    Create a new plugin file called ‘custom-activation-email.php’

    <?php 
/*
Plugin Name: Custom Activation Email
Plugin URI: YOUR URL
Description: Plugin to customize the automated user account activation email
Author: ME
Version: 1.0
Author URI: YOUR URL
*/
    add_filter( 'wpmu_signup_user_notification', 'kc_wpmu_signup_user_notification', 10, 4 );
    function kc_wpmu_signup_user_notification($user, $user_email, $key, $meta = '') {
        $sitename = get_bloginfo( 'name' );
        $blog_id = get_current_blog_id();
        // Send email with activation link.
        $admin_email = get_option( 'admin_email' );
        if ( $admin_email == '' )
            $admin_email = 'support@' . $_SERVER['SERVER_NAME'];
        $from_name = get_option( 'blogname' ) == '' ? $sitename : esc_html( get_option( 'blogname' ) );
        $message_headers = "From: "{$from_name}" <{$admin_email}>n" . "Content-Type: text/plain; charset="" . get_option('blog_charset') . ""n";
        $message = sprintf(
            apply_filters( 'wpmu_signup_user_notification_email',
                __( "Hi %s,nnThank you for registering with %s.nnTo activate your account, please click the following link:nn%snnYou will then receive an email with your login details." ),
                $user, $user_email, $key, $meta
            ),
            $user,
            $sitename,
            site_url( "activate/?key=$key" )


        );
        // TODO: Don't hard code activation link.
        $subject = sprintf(
            apply_filters( 'wpmu_signup_user_notification_subject',
                __( '%3$s - Activate your account' ),
                $user, $user_email, $key, $meta
            ),
            $from_name,
            $user,
            $sitename
        );
        wp_mail($user_email, $subject, $message, $message_headers);

        return false;
    }
?>

    Notes
    I’m using the ‘Theme My Login’ plugin, hence the changed links to /login and /lostpassword.
    I chose to do step 3 as a plugin instead of adding to my theme’s functions.php because I didn’t seem to work that way.

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