It seems a little unclear about the proper way to undertake this task. With the help of this group and the internet I have successfully built extension that integrate into the menuing system properly (ignoring project types I am not interested in), have been able to manipulate the menu items, and even store properties into the project file for use by what I lastly need to do. When I check this one menu item all I want to do is add a custom MSBuild task we have created. When they uncheck I will remove it. The question becomes what is the proper way to go about it. What I have found so far is modify the project file putting the MSBuild step in or import a custom targets file. Even on the latter I still cannot find anything to modify the project to do the MSBuild task. The closest thing I have found is a Hanselman or Buthrie video where they unload the project, use PS to modify the file, the reload it back. I am just trying to find the "proper" behavior that would be expected.
PS - We are not building custom project or flavors. This is stock WP8 project stuff.