Do you want to build these products say as normal products with unique descriptions, images etc and list this unique product in Shopify as you would any other product?
There are a few apps available that do custom pages in your theme that let users build products and checkout. If however you need the above it is something we do through our app. We create the unique products linked to whatever components they are made from. Then the quantity available is calculated of the component stock. When an order comes in for this product we can also update the order to show the individual components if required.
I'm Cindy, customer success from MyCustomizer, available on Shopify. Our app integrates seemlessly into Shopify with an iframe. It allows you to upload png images to build your custom product. Our user-friendly platform also allows you to link production codes and enter inventory quantities in Shopify.