I figured it out! I just use Apache's Action directive (http://httpd.apache.org/docs/1.3/mod/mod_actions.html#action)

AddHandler my-file-type .pdf Action my-file-type /scripts/scrip.pl

The filename headers I give the output does not change the Title of the file when displayed in the browser, nor does it change the default file name that appears in the save prompt when you try to save the file.