/etc/netscript/if.conf - interface setup shell script file
/etc/netscript/qos.conf - QoS setup shell script file
/etc/netscript/ipfilter.conf - IP chains filtering shell script file
/etc/netscript/srvfilter.conf - server IP filter shell script file
Please see the README file in the /etc/netscript directory, and READ the configuration files if you need to change them. Apart from network.conf, all of them contain sh (1) shell script functions which are there so that various things can be altered or hooked in at the right place. Network.conf contains the full network setup details, including special interface setup for the likes of ciped/pppd/wanconfig, and is fully commented with examples given.
The firewall/IP filtering stuff in ipfilter.conf is the part that changed radically with the move to iptables and a far better way of setting up the IP filtering rules, however the QoS and interface startup/shutdown in if.conf have changed but are backwards compatible with the old 2.2.x ipchains version of netscript for the interface address configuration settings. You will have to set up the filtering again to use iptables by directly using the iptables commands.
Also, the kernel 2.2.x version scripts are set up so that iptables is only run on a 2.4.x kernel, otherwise IP forwarding is disabled if beforehand you set IPFWDING_KERNEL to FILTER_ON in network.conf.
This means that when you upgrade a box to a 2.4.x router kernel, you should then be able to reboot it and log into remotely and upgrade netscript to the version that will support 2.4.x. In this situation, if you have set old IPFWDING_KERNEL setting to FILTER_ON beforehand in network.conf, all IP forwarding through the box will also be disabled. This means that you can safely remotely upgrade a firewall.