Thanks for the info. I suspected that splitting the two parts such that I handle the authentication based on the unique codes and the actual product purchase.
As you mention the part where I am hung is that I need to provide the unique digital code back to the end user upon completion of the purchase. At the moment I have a custom built set of code that does this, but I really want to move the site to WordPress and was hoping to avoid having to write a bunch of new code to integrate into WP.