You need to make sure cgi is mapped to perl and permissions are set as in the docs on the files and folders containing the files.
I'm not sure how changing the extension to .pl will make the script more secure, but modifying the files like that *does* make your forum installation unsupported by groupee.
The best way to make sure your site is secure is to keep your software updated (IIS, perl, php and forum scripts) with the latest stable code.
Make sure servername_everyone has full permissions on the noncgi and the variables directories - it's been a while since I ran classic on a windows server, but it can do a great job if setup right <img src="https://www.ubbcentral.com/boards/images/graemlins/smile.gif" alt="" />
