Ah, I see then. So the mod was to give a more historical flow to the gameplay outside the players control. Very good then. I do have the mod downloaded, and once I do feel more comfortable with the game I'll try seeing if it will work with the Matrix version of the game. If it doesn't, I can always just re-install.
I have yet to really play more than a few decades in a couple of scenarios as I'm still working my way through the expanded rules, but I can already see the gem that this game really is. The brilliance to me is in the choices of 1) multiple country play per side 2) the Barbarian, Kingdom, Empire rise and decline mechanics 3) the solid layout of the ethnic and religious systems and their importance in the game as in history and 4) the entire strategem concept allowing the player to try and outwit or bend the fates to his side. The blending of these 4 main concepts I believe fit this chaotic period of European/North African/Middle Eastern history like a glove as well as make the game fun to play. Very well done indeed!
The sad thing is, I can see that back when this game came out, many people seemed disappointed with the concept of not running just one state. The idea of playing multiple countries to the best of your ability each to score points, rather than try to achieve some kind of non-historical empire with one country is hard for some people to grasp. I well remember the difficulty many of my friends and I had many years ago when we first came across and played the game Britannica, which uses a similar system. Yet with some practice and experience, one comes to appreciate the nuances of such a system, as well as how well it can be used to balance a game. This balancing ability is even more in evidence in Great Invasions with the very nice bidding system. Unfortunately, it seems a lot of people and reviewers came into this game expecting another form of Europa Universalis, which with all it's strengths in depicting the Medieval world onward, just doesn't work for this particular period as well.
Well, I look forward to enjoying many hours with this game, and I'm going to introduce it to my local board gaming group as well. One couple are already interested in the game now from what I've told them about it, and if all goes well, we may see about trying out a LAN game of this. I hope that someday you do seriously consider giving this game another chance at life with an updated version, because as I said, I think you really hit on an excellent formula for depicting this rather neglected era of history.