Will, for the registration problem, have you enabled "Email Based Self Registration" on your site? Generally and by default I think Manual is the only enabled method. This will allow users to create their own accounts.
As far as an org vs. individual setup, you might consider having the "Org" product be a different course that just includes a survey (to register their users) or a posted enrollment key that they can share with their employees. The "Individual" product would be the course which is accessible via paypal enrollment (for those without the enrollment key, or the enrollment key [no cost]).
It's not as safe as simply using Paypal enrollment but it would accomplish your general goal I think.