For security reasons, Apache turns off symlink following by default. This prevents people from doing things like grabbing sensitive files and such.

Maybe what you need is set your Options:

Options +FollowSymLinks

This can go in your .htaccess if you are allowed to override it. This could require modifying your base httpd.conf file to allow this. I usually just let anyone do anything on any server to which there is controlled access:

AllowOverride All

What might also be causing the trouble is that your script is no longer inside the /cgi-bin directory. You might need to assign the proper handler:

AddHandler cgi-script .cgi

For mod_perl this would be, of course, perl-script.