1. The duplication happens because you have a menu content block in your footer region. Remove it.
2. Drupal manages the content that is being linked to from the menu, so it will always have more data. The principle should be to expose that data to ckan.

As for the suggestions, we can remove some outer markup, but isn't a <footer> tag a standard markup element for a footer? The other markup/classes is there to preserve some standard styling. Happy to remove it, but you will need to replace/override any styling logic.

We won't need to move render($page['footer']) as content will only appear if we add content there.

Drupal can provides individual classes per menu item as default. have you looked at them?