Hi,
Well, my answer still answer to your problematic:
when sending them the email, you can use such link:
yourwebsite.com/index.php?option=com_hikashop&ctrl=order
so that they can access their orders listing.
If you activate the "Payment of orders not paid immediately" setting of the HikaShop configuration, they will have their a pay button for their order. And you can configure the status in the menu System>Order statuses if you don't want them to be able to pay their orders from that page before you reviewed their order.
if you do just that, without changing the checkout workflow, you be able to have people purchasing normally your products on your checkout, and you'll be able to create custom orders in the backedn and give a link to the customers so that they can pay for them on the frontend once you've negotiated with them.