Hi,
Edit the email via the menu System>Emails.
There, you can add the tag {VAR:order.order_number} in order to add the order number in the HTML version of the email.
And regarding the custom order fields, you would have to change the line:
echo $sep . $fieldsClass->trans($oneExtraField->field_realname).' : '.$fieldsClass->show($oneExtraField, $data->cart->$fieldName, 'user_email');
to something like:
echo $sep . '<strong>'.$fieldsClass->trans($oneExtraField->field_realname). '</strong> : '.$fieldsClass->show($oneExtraField, $data->cart->$fieldName, 'user_email');
in the preload version.