How can I turn a list of Aliases into a menu structure?
I'd give the Menu Export/Import module a go.


  This module helps to export and/or import menus. Using it you can
  easily copy menus from one Drupal site to another.
  
  It also allows developers to quickly build a new Drupal site by
  creating empty content and menu items referencing it. The module may
  be used in ensemble with Node export that allows to add content to
  your Drupal site. In this case, menu import allows to batch-arrange
  existing content into a given menu structure, using a very simple text
  file.


I guess you could possibly use Excel or something to take your list of aliases and split the paths to columns which would give you the menu title (in the last column of the split).

From there you have the menu link titles and paths, so it's just a case of getting it into the format that the module expects.