Must say I've had an absolute nightmare intsalling this mod. Funnily enough it was mostly my own fault for getting creative with some of the problems. Firstly, I tried to install the automatic installation, but the rig I've got fallout installed on is an ancient AMD 500mhz win 98 machine. Everything installed ok up until the end when it tried to access my master.bat file. The master.bat just wouldn't be modified. It's stopped me being able to save ingame. Afterwards, I tried to install the manual version, but ran into the same problem of not being able to save the game. When I shifted things around again I found I could save the game, but half of the new quests were broken and would either not start at all, or be impossible to finish (this would be around the time I started to imagine the violent deaths of the mod creators...).
So after days of banging my head against the keyboard and stubbornly searching the net for answers, I finally managed to piece everything together and get a proper install. I think the issues were that the first install was still in the registry and was cocking up later installs (I fixed this with an old version of CCleaner). The master.bat file would still not install properly, so I had to do the last bit of the installation manually (thanks to the information of a poster on this forum). I'll repeat it here so it's clear for anyone experiencing the same issue.
When you've unpacked the batchwork folder (I'm assuming you're using the manual installer and win 98) into your main fallout2 directory you access the same directory via MS DOS prompt. When you've reached the folder you type each line individually making sure you press enter after each line of code. You'll get a blank screen popping up for a split second. When you've done all four the master.bat file should be modified (you can check the file, but you won't get any other type of verification).
START dat2 d master proto\CRITTERS\00000502.pro proto\CRITTERS\00000503.pro proto\CRITTERS\00000504.pro
START dat2 a master proto\CRITTERS\00000502.pro proto\CRITTERS\00000503.pro proto\CRITTERS\00000504.pro
START dat2 d master proto\CRITTERS\00000089.pro proto\CRITTERS\00000079.pro
START dat2 a master proto\CRITTERS\00000089.pro proto\CRITTERS\00000079.pro
Hopefully, this post will make it clear to anyone experiencing similar issues and they can avoid a few days of head banging. I'm not sure if this would work if you're trying to use the automatic installation on win 98.
Thanks to Killap for a great mod!