Hey Kevin!
Thanks for reaching out on the forums!
Perhaps getting your customers to call in their product information might be useful? You could also just use a basic contact form to get them to reach out to you, even creating this with a free app- https://apps.shopify.com/improved-contact-form. Wufoo- http://www.wufoo.com/ might be another good free option, to help you create a submission form to add to your store! You could also include the amount they want you to pay in this information, and you could then use this to make the document for when you pay them! This kind of service sounds like something that would be managed seperate to your order admin, as you are not using the product/ cart or checkout section right?
For the second part, you sell product parts that are often used as part as your service, right? And you want customers to be able to buy a product that includes some of this stock and have the inventory sync, would that be correct? Please let me know and I can see what options may be out there for you!
Warm regards,
Anne :)