Lets try the following before you go down the route of paying us for custom development. This is kind of a workaround/hack so it may not be exactly what you want but its worth a try.
1. Use a contact form plugin such a contact form 7 to create a custom form that you can use to collect all the details you want from your customer.
2. Place this contact form on a WordPress page on your site.
3. Tell eStore to send the user to this page when they do manual checkout (you can specify it in the manual checkout settings).
4. Add a shopping cart shortcode on your sidebar or on the page where you have the contact form (just above the form will do).
This way when they are filling out your custom form they can see the shopping cart which will display all the items they are purchasing.