Running your own Add-ons server will likely require a few changes. There is currently no easy way to provide custom templates and since Firefox Accounts is used for authentication there is no way to authenticate a user outside of a Mozilla property.
If you would like to run your own Add-ons server you may want to update addons-server to support custom templates and move the Firefox Accounts management to a django authentication backend.
Another option would be to add any APIs that you required and write a custom frontend. This work is already underway and should be completed at some point but help is always welcome. You can find the API work in this project and the frontend work in addons-frontend.