How to store css & js in separate file & call in custom 'tpl' files through variable in drupal 7?
If you do not want, or are unable, to modify the theme html or page templates, you can also use drupal_add_css and drupal_add_js in the page_callback function defined in your modules menu array youmodule_menu().

If you have access to the template.php of the theme,  you can use the preprocess hook to assign a variable to the file name, then do an include in the html template.  Or from within your module use drupal_add_html_head, but this has limitations.

Using drupal_add_(css|js) the links go into the head element of those pages by default before the themeing phase begins, but you can also specify the boostrap phase and location.

EDIT

Using drupal_get_path from within yourmodule_init hook or the page_callback, and with the css and js stored within your module structure, you can then add the css and js using the drupal_add functions.  This makes a single place you need to maintain the 'paths' to the files.