Welcome to the Shopify Community! One suggestion is to use a digital download app from the Shopify App Store.
You can create a digital product, specific for this customer / order. You can also set the price of this product, for example, $0.00 if the PDF is free, or you can charge a price for it. Once you've downloaded the app, and created the product, you'll be able to add this digital product (just like any other product) to the order when you create a draft order (Shopify Admin > Orders > Create Order). Your customer will be able to download the PDF via an automatic email that is sent once you fulfill the order. Here are a couple app options:
Let me know how this goes, and if this solution works for you!
Hilary | Community Moderator @ Shopify - Was my reply helpful? Click Like to let me know! - Was your question answered? Mark it as an Accepted Solution - To learn more visit the Shopify Help Center or the Shopify Blog