WooCommerce - Apply Coupon Discount to custom orders.

Hi

I need to apply coupon codes applied on /checkout/order-pay (form-pay.php) to be applied to the price of the custom added order.

I added code to form-pay.php to show the button/form to apply coupon. When coupon is added it shows 'coupon applied' or 'Coupon code already applied!' but doesn't actually effect the order total for that custom order page (/checkout/order-pay/12345/?pay_for_order=true&key=order_example12345

Ideas on how to get it to apply the discount successfully to that order?

The form-pay.php code: http://pastebin.com/TAd9zgZh

Cheers!