Need help in delay payment and manual enter shipping cost.

Hi all,
Firstly, thanks in advance for all who read this and tried to help me.

Currently, , I'm using 1.3.8 on Linux platform.

Here is what I wish to do:

1. After customer make an order on my site, they will "temporary" check out.
2. I will receive notification and go to my admin module to check his order.
3. I will set those item which i do not have stock to "zero" and enter the shipping cost
4. Customer will get notification on the "updated" order and make payment.

How, can I achieve above, especially, I found that I cannot alter the order and delay payment only till I had confirm the shipping cost.

I have such situation because, my stock may run out when multiple customers purchase the same item online as well as offline. My offline store inventory do not link to ZC and as such, will not be able to detect in-time if online customer have already made the order. So, I need the ability to set it to zero if, unfortunately, my stock is exhaused on my offline shopfront end.

I do not know the exact shipping cost and will need to know the "final" item available and added the shipping cost based on weight and boxes. So, I need to do manual calculation, especially if some item is out-of-stock and I will need to exclude them.

Thank you again in advance.

Regards,
Matthew L Bird