The only way this can be achieved is by getting an e-mail delivered to the customer automatically when they purchase your product with a "Download PDFs" link in that e-mail. Then, when the customer will click on that link, he will be taken to a page that I can code, which will ask them for the PayPal transaction ID and their e-mail address. Once they enter this info, they will get the unique PDF files.
We can not make changes to eBay functionality but we can work this way and achieve the required objective. Let me know what you think about it.