Нашел решение)
$order->add_product( get_product('4534'), 1);
$order->set_total(40, 'shipping');
$order->set_total(0, 'cart_discount');
$order->set_total(0, 'cart_discount_tax');
$order->set_total(0, 'tax');
$order->set_total(0, 'shipping_tax');
$order->set_total(40, 'total');
