The front page only shows "recent questions and answers" so is not paginated. I think you can make the front page show the same as /questions by doing this:
'questions' => '',
But I haven't tested that.
Edit: as for copying the links at the top, that is done in an advanced theme. In the main() function, you'll see $this->page_links() towards the end. Just copy that line and put it further up, anywhere above main_parts() should work.