The two northern cities are good. In order to block, you want them to take up as much space as possible, and you're right that they have good land, too. You can settle a city for overlap later.
Your city placement crime was ignoring all three seafood resources. One food resource is all you need for a decent city because that's enough to whip for production and run specialists. If it has a few more mediocre tiles, like coast, that's even better. The point of overlapping is to work as many tiles as possible, so really the first thing you want is to have as many tiles as possible within the fat crosses of your cities. Getting enough citizens to work all those tiles is second priority, and that's where overlap comes in. So spreading out to get those seafood resources is a good thing.
Right now, the thing you need to do to work more tiles is to fix your happiness problems. Did you recently switch out of hereditary rule? That may have been premature since you don't have many towns. The best you can do now is to get a fishing boat onto those whales, trade for wine, and cash-rush markets for four happiness.
You could specialize your cities more. Your specialist farm is the right idea, but that usually works better with a few great food tiles, instead of many floodplains. It takes too much population to work all the floodplains and run specialists, which is a problem when you're limited by happiness or health, and the floodplains make the health even worse. Floodplains generally get cottaged, and a better location for your specialist farm would have been the crab+corn+sheep location in the southwest. That city could run 4 specialists at size 7, and more once you get irrigation down there.
For more specialization, you need one more cottages in general, but one city should have no cottages and specialize in production. Build the heroic epic there (one of your priorities while hunting barbarians should be to get a unit to 10 exp so you can build the HE).
Markets and banks don't directly help with science, but they do increase your gold income which allows you to increase the science slider. If you are already running high science, then the banks don't help much. But do build a bank in your shrine city because the shrine gives gold which isn't affected by the slider. And you want markets for the happiness and gold is also useful for rush-buying and upgrading, so you should build banks eventually.
You're doing well versus the AI in your current game, and you're already beyond the typical newbie advice, which is to build more workers. Though you need to keep them busy building improvements before the cities grow, and changing existing improvements to fit your current needs. OK, I hope that helps.
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