I can see the problem with such a high civ number and populations over such a long period of time compacted onto small region would quickly allow a strong civ to overpower another.
That being said, I'm not too knowledgeable on the subject of world gen.
Another problem is that civilizations such as humans and elves will not settle in certain biomes, such as evil and of course they will avoid certain tiles such as mountain peaks and ocean and possibly extreme temperatures, so you've basically got 40 civs crammed into a walnut.
Your best bet would be to experiment. That uberhigh total_civ_population isn't entirely necessary. (You won't ever notice them in adventure mode or in fortress mode). Perhaps tone down the total number of civilizations. An absolute bet would be to lower the year end number. You could also try increasing the world size. Remember that the settings that are default are default for a reason, and trying to cram a large region's content into a small region's space, while not always reject-causing, can lead to undesirable results. I don't mean do EVERYTHING I said, you don't have to tone everything down, but you SHOULD try experimenting if you don't like my suggestions and try to get a compromise between your desired results and a successful world gen recipe.
Also, do you get rejects? Set your init file to log rejects if you do and find out what is causing rejects at what point in time. I won't say it'll tell you exactly what's wrong, but you might get a bit of useful information here and there. (Most rejections are from failing to meet land qualifications, I don't know if you can get rejects for a civ requirement not being met)
That's all I've got.