Need to manually regsiter user, send the password and retreive their user ID

If you want to force add a MU user and activate them, and email them, this will do it. It’s a slightly altered version of a piece of the code in user-new.php.

wpmu_signup_user( $new_user_login, $new_user_email, array( 'add_to_blog' => $blogid, 'new_role' => $role ) );
$key = $wpdb->get_var( $wpdb->prepare( "SELECT activation_key FROM {$wpdb->signups} WHERE user_login = %s AND user_email = %s", $new_user_login, $new_user_email ) );
$ret = wpmu_activate_signup( $key );

The wpmu_activate_signup function will send the welcome email. And the $ret from wpmu_activate_signup is an array of several things, including the user_id in $ret[‘user_id’].

Obviously you’ll need to fill in the user name, email, blogid, and role in the above code.