After I replaced the network interface, when I ran an ifconfig -a the new network card was showing up as ETH2. This is a problem as all my firewall scripts in IPTables was written to reference ETH1.
The physical NIC referencing such as ETH1, ETH2 and ETH3 in Ubuntu linux is stored in a file called 70-persistent-net.rules which is located under /etc/udev/rules.d/70-persistent-net.rules
After cracking open 70-persistent-net.rules we see the 3 network interfaces. The first two were setup when I installed Ubuntu. The last interface, ETH2 was setup when I installed the new network interface in the PCI slot.
I simply added the MAC address from ETH2 which in my case was 90:F6:52:00:51:65 to the already existing entry for ETH1 and removed the ETH2 entry from the configuration file.
After making these configuration changes a reboot to the server was required. After the server rebooted, the new network card took over the old ETH1 interface and all my firewall scripts worked correctly.