63272 Linux Server setup

We have a root server running with Red Hat 9, Apache 2.40, perl 5.8, PHP 4.3.9, MySQL and Plesk 7.14 or so... all pieces of software are updated with Yum. We have 2 problems as we are not linux gurus...: - we get servor errors while trying to run CGI/Perl scripts and rewrite_mod features. This is NOT a simple problem of perl path or chmod... we looked into it already. - we need to setup our iptables for protection and to let remote mysql working. We will provide root access through SSH for the duration of the project... This box is in partial production Thank you