For external connectivity I would suggest using scenario 4 in which a static IP is assigned to the z/OS box(s) and it communicates to the network with its own IP address (and to Linux via the tunnel only). Then the connection is a direct connection from W2K8. If you have a static IP for the z/OS box on the same subnet as Linux (which it may need to be anyway), you can use the create_config.pl script on the samples disk to see what the TCP/IP and VTAM definitions should look like. The caveat is that the suggested changes may need tweaking for your network but so far such alterations have been minor for those that have used it.
It looks like Scenario 3 covers port forwarding of incoming connections, so start there if you want to keep the setup you have more or less. Issues with iptables include port conflicts and problems with products that dynamically assign ports such as FTP and RDz and several others.
Another option for passthru of 3270 connections: the way I have done that is with an SSH tunnel and port forwarding for specific ports like 23->3270. That goes to the local terminal but I think you can forward to other IPs. An SSH tunnel is fine, if a bit clumsy, as long as you know the ports you need in advance and have an account on the Linux box.
SystemAdmin