Thank you for your comment, I'll annotate all your suggestion and try to fix the issues if possible.

About the issue when installing the addon, it requires all the opened pages to be reloaded after installing the plugin (it is necessary because it has to inject the code that creates the annotations). Maybe you reloaded (or rebooted) Firefox after saving the configuration (it would be great if you could confirm this, as I can´t reproduce the issue in my navigator).
About the source code, it is posted in github (https://github.com/carriH/My-Notes). Please, let me know if you still can´t access to it. Thanks.