I think you may have to check the 'time limit' box and enter the number of turns (989 for the numbers you have listed), otherwise the game may still stop after 540 turns (notice that 540 is still shown). I'm not sure, someone would need to test this.
If you want us to critique the years breakdown, perhaps you could post for us when the actual years (instead of turns) would happen--For example:
7000 BC-start, 1 turn=40 years for the next 31 turns
5760 BC, 1 turn=30 years for the next 50 turns
4260 BC, 1 turn=15 years for the next 100 turns
2760 BC, etc.
Unless you REALLY slow the tech pace down, it looks like you would have some pretty outrageous circumstances (like lauching spaceships in the BC years).