How can I override the autocomplete.js file while developing a module? I want to override the default tags field wherever it is used. After looking through a few files, I figured that I should override drupal/misc/autocomplete.js and the Drupal.jsAC object.

Is it correct to override this file, since I only want to work with tags field?
How is it possible to create a module which overrides this file?
As long as all you want to do is achievable by using form_alter() and #autocomplete_path, you should avoid modifying core's JavaScript files. To address specific field widget, use hook_field_widget_alter().

If you need to alter what JavaScript is doing, use corresponding behaviours, as described on StackOverflow.