I came across the same problems and so I made my own interpreter for the peerguardian script which made a bash script to run the iptables commands. I cannabalized this bloacklist converter program to do this, take a look if you like:
just download the latest peerguardian guarding.p2p, run it through the converter into iptables format, and run the bash script. I don't think there's any customising neccessary. I actually expanded this quite a bit further, including an IP.Prefix file and IPFilter for eMule, al of which were combined and then added using a seperate chain that could be run on input, output and forward, and would auto-update hourly using cron, but this program is the essance of it - you shouldn't have too many problems just using this once or occasionally or even designing your own script. I haven't got anywhere to upload mine atm sorry.
hope this helps.