PHP Code:
  <li><?php $content .= '<a href="' . zen_href_link(FILENAME_SPECIALS) . '">' . CATEGORIES_BOX_HEADING_SPECIALS . '</a>';?></li>
The $content .= part is used in tpl_categories.php, where content is accumulated before being output. Here it is output directly, so you would want to change
$content .=
to
echo
PHP Code:
  <li><?php echo '<a href="' . zen_href_link(FILENAME_SPECIALS) . '">' . CATEGORIES_BOX_HEADING_SPECIALS . '</a>';?></li>
Do the same for the other link.

For the sidebar, I didn't check to find that you were using the left sidebar already. That makes it easier; you can just enable the categories box in the left column, set its width and a negative margin-right if needed (it may well not be needed), and move the box to the right with position: relative; .

The category ids can't cause any problems. Just use the cPath if needed to specify a category. Your case is actually very simple, and you don't need to mess with groups at all. Setting the top cats to be hidden in categories_dressing_defines.php means that you will want to move the entire remaining content of the box to the right-side position.
You will also want to disable or hide the subcategory links on pages that are not subcat listings.