Typically, scripts would be placed in cgi-bin, not cgi-bin/perl, but that shouldn't make a difference.
If the script is under cgi-bin and has execute permissions (you should change the permissions to 755, by the way), the most likely suspect is the server configuration. ScriptAlias isn't configurable in .htaccess, so you can't set that yourself. Log in to cPanel and go to the CGI Center options; you may be able to enable CGI support there.