This is indeed much better than the first save you posted.
More Things to Consider
In Washington and some other cities, you have hired Entertainers. Generally, those guys (clowns) are the worst choice to make when you hire specialists. Washington is at size 12, so it cannot grow, though it does have a lot of extra food. Here, by firing the clown and working the last grass tile, commerce from the city increases from 45 to 50 and the gold-per-turn from Wasington goes from 28 to 33. In turn, your gpt overall increases by +5 gpt. More money in the bank.
In Austin the situation is different. This city is corrupt (netting one shield per turn at size 6) and it has a clown, too. It is building a Longbow, but has no barracks, so that Longbow will be a regular unit, not a veteran. A better build would be a trebuchet, which are unaffected by barracks, and cost less than a Longbow. This city has all the improvements it needs, since it is too corrupt to be really useful. It would be a good science farm. Even now it produces 3 extra food. If the citizen on the tobacco works the irrigated grass tile, it now produces 4 extra food. If the clown becomes a geek, that geek adds 3 beakers to turn to your research, which drops Gunpowder down to 8 turns from 9.
In New York, which is moderately corrupt, you have a barrcks and are building a Longbow. The city nets 4 spt and starts with 9. A courthouse might be in order after the Longbow, to reduce that corruption a bit.
Philadephia is building a colosseum. You really won't need that build. As you get more adept at city managment, you will become better at keeping your cities happy and productive, and the need for the colosseum will go away. The city already has a market and doesn't need a courthouse. A granary would help grow it to size 12 and you would only lose 13 shields.
Flagstaff is a renamed city captured from Maya. All the citizens are Mayan. Here, make everyone a geek and don't worry too much about the rioting. I would change the settler build to a worker, since this will be a Worker (Mayan) (a slave) and cost you nothing in per turn upkeep. As a settler, when it becomes a city, the first citizen will be Mayan, and right now with a Mayan war, you probably don't want that. In later turns, I would let let the city get one shield invested in the next worker and then rush that worker for 36 gold. I would only use enough citizens to keep the city from starving; everyone else would become a geek to help with research. Keep doing this two turn cycle and the city will soon be down to size 1 and much less likely to flip back to Maya. And you have a bunch of slaves to help your workers. They are slower, true, but they can be grouped into stacks of 6 or 8 to road/irrigate in one turn.
You have an MGL, Washington, outside of Lagartero of Maya. Washington is fortified. Umm, not a good idea. As long as you have one acitve MGL, you cannot generate a second one. Veterans will promote to Elite (I think) but Elites will not become Elite*. Wake up Washington and move him into Flagstaff and then build an Army with him. It can be filled later. Once Washingto is used, you have a chance to get another MGL and form another Army.
You have a lot of jungle in your core. That has got to hurt. As IND jungles take 16 turns to clear. I would group 4 workers into a stack and have them start clearing the stuff out. Four turns to clear a jungle tile is pretty good.
Once every few turns, whatever feels right to you, cycle through all the cities and look for ways to improve their output. For a science farm, which only nets one shield per turn, it makes no sense to have a citizen on a mountain when it could be on an irrigated grassland helping the city to grow. At first you won't see much you can do to make things better but eventually you will.
Summary
Once again, this is a much better game than the prior save. And what I have noted are some things that you are probably too overwhelmed to consider. I know how pressured I felt when I left Chieftain. Scarey! But you should be up to Monarch/Emperor in no time.