This is an interesting project. It's too bad GIS data only exist for modern terrain, not ancient. But for your animation, you won't need the old GIS data. I'm about to embark on making a series of scientifically based reconstructions, from post ice age to medieval times of one village + surroundings. I can get GIS data (though never used them before), but the ancient terrain must have been quite different (streams changed their flow, etc).
Looking forward to see you develop this...