Nice job! I haven't looked at it yet, but more flexibility is a good thing.
One comment: the description says
"This mod will replace your existing modules/sideboxes/categories.php, and templates/template_default/sideboxes/tpl_categories.php files. The original files will be renamed with .old"
Does this really mean that the original files are replaced in their original locations? The right way to do something like this (except in the few places where the override system does not operate) is to have the new versions in an override folder structure with a placeholder template name like /your_template/. This will require the user to edit the folder name before uploading, but is the correct method for adding custom functionality.
So you would have
/includes/modules/sideboxes/your_template/categories.php, and /includes/templates/your_template/sideboxes/tpl_categories.php
No need to save .old copies of the originals, and the mod files are safe from being overwritten in upgrades.