I recently needed to alter the address fields within the Ubercart 3 billing pane. Unfortunately, due to the way Ubercart 3 builds these form elements, the standard hook_form_alter() hook was not going to work. After a few hours of searching I finally discovered this post:
https://drupal.org/node/2063949#comment-7750227
With that information I was able to alter my billing pane's company field into a select list taken from a taxonomy.