hook_modules_enabled called before hook_menu
So, here's the solution. Hopefully it helps save someone else some time. As it turns out, hook_menu() is not invoked during module enabling. As such, I had to force a menu rebuild which invokes hook_menu() and ensures all the proper routes exist prior to building my menu links.

base.module>

/**
* Implements hook_modules_enabled()
*/
function base_modules_enabled($modules) {
  menu_rebuild(); // &lt;--- Added this line to force hook_menu() to be called first
  $links = [];
  foreach ($modules as $module) {
    $module_links = module_invoke($module, 'operations_menu');
    if(is_array($module_links))
      $links = array_merge($links, $module_links);
  }
  foreach ($links as $link) {
    menu_link_save($link);
  }
}