Without looking at the logs to try and understand the history of this game in detail --
Looks like you've gotten a few great people. Not as many as one could, but you've gotten a few, that's cool.
To answer your question about great people, if you want a really simple way to ensure that you get some great people, build a city that can work a high food tile (fish, pig, or wheat or corn next to a river or lake), build a library, and at size 3, hire 2 scientists, and never fire them. Keep checking on the city, because if it grows, the computer might automatically fire one of the scientists for you. That is a method which is real simple yet will ensure that you get a steady steam of effective great people starting early. If you have the food to spare, do it in two cities instead of one.
Great Generals are generated differently and separately from other great people. When you win a fight and gain experience points you accumulate points in the Great General-O-Meter, which you can see in the Military Advisor (F5).
Looking at the map it looks like you should keep in mind that every city must be "supported" by one or two good food tiles. Example 1: Ankara should have been built 2 tiles west. The cows and farmed flood plains (and the extra flat grasslands) would allow it to work the 2 gold mines and still grow. Example 2: Nagasaki sucks. One E of where it is would be much better, then it could work the rice and the gold. Nara sucks too, because it blocks the gold and rice from being worked usefully. Ideally, if you can afford the settlers etc., you'd raze both cities and rebuild them with better city placement.
Also, you should take my advice to make some of your cities (at least one!) a production city, with no cottages, only mines, farms (and pastures and work boats etc), and (later) workshops. Build Heroic Epic there (build it somewhere!) All cities need to have high food, but production cities especially need to be high-food so that they can work low-food / high-production mines and workshops.