We are talking to a number of people about creating their own custom learning environment using the Khan Academy open source code base. We currently have a clone of Khan Academy set up as part of our integration with Moodle. On this clone we can access the administrator pages and we can show you the tools that Khan Academy uses to manage their content.
This video shows a quick tour of the tool for managing the content map. You will see a straightforward UI that allows administrators to add new YouTube Videos and exercises. Thus once you have a clone of Khan Academy it is definitely quite possible to add your own content and rearrange it to create a custom learning experience.