David,
Thanks for sharing your question the community. I admit, I don't know Joomla that well to be able to suggest a solution, but I do have a few ideas on how this could be done to help alleviate the workload for you and your business.
You could create different Web Forms and set various actions on those to add Tags that describe the "level" of access that one has. From there, you can pull those tags and export into a Mail Merge so you can print (or have a company) print those certificates for you.
As far as setting up a paid-course system, it's similar to the Web Form example above. You could use Order Forms where you sell tickets. On the success actions, you could indicate sending a mail template, adding a tag and even make use of the fulfillment list feature so you can print separate certificates.
The next thing is to be able to provide a means to how people can access premium content and stuff on your site. This is where I become fuzzy. There is a Joomla integration from Infusion Alliance (a CMAC partner of ours) where they have a free and commercial solution to link up user registration and restrict access to various tags and levels in Infusionsoft.
I hope this helps or adds clarity to what you're looking to do. Let's keep this alive and discuss it more and I'm sure people will be happy to chime in with their ideas.

~Joe