Cracked it! 
Info for anybody wanting to do the same, I altered after line 103 of admin/orders.php where it says // send emails.
It now looks like this
Code:
if ($status == '3') {
$message = STORE_NAME . "\n" . EMAIL_SEPARATOR . "\n" .
EMAIL_TEXT_ORDER_NUMBER . ' ' . $oID . "\n\n" .
EMAIL_TEXT_INVOICE_URL . ' ' . zen_catalog_href_link(FILENAME_CATALOG_ACCOUNT_HISTORY_INFO, 'order_id=' . $oID, 'SSL') . "\n\n" .
EMAIL_TEXT_DATE_ORDERED . ' ' . zen_date_long($check_status->fields['date_purchased']) . "\n\n" .
EMAIL_TEXT_STATUS_UPDATED . sprintf(EMAIL_TEXT_STATUS_LABEL, $orders_status_array[$status] ) . "\n\n" .
strip_tags($notify_comments) .
strip_tags(EMAIL_TEXT_DELIVERY_INFORMATION) . "\n\n" .
EMAIL_TEXT_STATUS_PLEASE_REPLY;
} else {
$message = STORE_NAME . "\n" . EMAIL_SEPARATOR . "\n" .
EMAIL_TEXT_ORDER_NUMBER . ' ' . $oID . "\n\n" .
EMAIL_TEXT_INVOICE_URL . ' ' . zen_catalog_href_link(FILENAME_CATALOG_ACCOUNT_HISTORY_INFO, 'order_id=' . $oID, 'SSL') . "\n\n" .
EMAIL_TEXT_DATE_ORDERED . ' ' . zen_date_long($check_status->fields['date_purchased']) . "\n\n" .
EMAIL_TEXT_STATUS_UPDATED . sprintf(EMAIL_TEXT_STATUS_LABEL, $orders_status_array[$status] ) . "\n\n" .
strip_tags($notify_comments) . "\n\n" .
EMAIL_TEXT_STATUS_PLEASE_REPLY;
}
$html_msg['EMAIL_CUSTOMERS_NAME'] = $check_status->fields['customers_name'];
$html_msg['EMAIL_TEXT_ORDER_NUMBER'] = EMAIL_TEXT_ORDER_NUMBER . ' ' . $oID;
$html_msg['EMAIL_TEXT_INVOICE_URL'] = '<a href="' . zen_catalog_href_link(FILENAME_CATALOG_ACCOUNT_HISTORY_INFO, 'order_id=' . $oID, 'SSL') .'">'.str_replace(':','',EMAIL_TEXT_INVOICE_URL).'</a>';
$html_msg['EMAIL_TEXT_DATE_ORDERED'] = EMAIL_TEXT_DATE_ORDERED . ' ' . zen_date_long($check_status->fields['date_purchased']);
$html_msg['EMAIL_TEXT_STATUS_UPDATED'] = str_replace('\n','', EMAIL_TEXT_STATUS_UPDATED);
$html_msg['EMAIL_TEXT_STATUS_LABEL'] = str_replace('\n','', sprintf(EMAIL_TEXT_STATUS_LABEL, $orders_status_array[$status] ));
$html_msg['EMAIL_TEXT_NEW_STATUS'] = $orders_status_array[$status];
// $html_msg['EMAIL_TEXT_STATUS_COMMENTS'] = nl2br($notify_comments);
// <---- Start Edit ---->
if ($status == '3') {
$html_msg['EMAIL_TEXT_STATUS_COMMENTS'] = nl2br($notify_comments) . nl2br(EMAIL_TEXT_DELIVERY_INFORMATION);
} else {
$html_msg['EMAIL_TEXT_STATUS_COMMENTS'] = nl2br($notify_comments);
}
// <---- End Edit ---->
$html_msg['EMAIL_TEXT_STATUS_PLEASE_REPLY'] = str_replace('\n','', EMAIL_TEXT_STATUS_PLEASE_REPLY);
Also added a line into admin/languages/english/orders.php
Code:
define('EMAIL_TEXT_DELIVERY_INFORMATION', 'Delivery Info Goes Here');
Ive moved the comments to below the order status in the email updates, the text is done above and the html by altering email/email_template_order_status.html to suit.
Hope its useful to somebody! There is probably a better way to do it I didnt find but feeling good about it myself, will update the live site tomorrow