What is the ruling on taking money through selling digital files (PDF) of journals via Amazon, where Amazon prints and ships the product after the order, and the price is paid before delivery, with the seller only owning the digital file? Does this fall under selling what one does not possess, considering that Amazon takes a fixed percentage of the price?

There is no objection to this transaction. Amazon acts as a paid agent for the questioner in selling, printing, and shipping the book to the buyer, and the fee is known. The company's sale of the book falls under the category of bay' al-salam (forward selling) — which is the sale of a described item with deferred delivery — and does not fall under the prohibition of selling what you do not possess. Its condition is that the buyer pays the full price at the time of the contract, which is what we understood from the questioner's statement: "The buyer pays the price before delivery."