ISPConfig runs as Apache2/PHP5 on port 81.
ISPConfig runs Apache1.3. So you already have 2 apache versions.
You need to build/compile a new apache2/php5 instance manually from source. The apache/php websites show detailed instructions how to build from source. Make sure you don't
accept the default install directories, but choose your own. Next change the new apache.conf (in your custom directory to listen to a different port. And as a last step, you can do proxy forwarding to masquerade the alternative port.
It's quite some work...... If it's only one script, maybe updating / modifying that script is easier.