Not checking the save, as vanilla is acting up and I'm playing only warlords games myself anyway. Been hitting some graphics bugs, so probably will have to do full reinstall (and maybe update graphics card drivers) some day too.
But going from the screenies..
My basic idea is that working FP=3 tile is not useful unless it's a grassland farm that is required to provide food for something or other - but that something or other better be worthwhile then. Combination of grassland farm and grassland hill mine is F=4 P=3, which comes to 1.5 hammers per citizen - acceptable total result.
I'm a lumbermill freak, which means I often leave several forests alone waiting for replaceable parts. Lately I've been chopping more aggressively though, as the early game hammers are a big deal. Still, a forest waiting for lumbermill is a production city issue, commerce cities will have their forests chopped and replaced by cottages at whatever rate they need new cottages.
You're building commerce improvements in all major cities. Some city specialization might be in order - a city that isn't producing at the very least 20 base commerce at this phase doesn't need them. I would say that targeting 6 cottages is absolulte minimum for a city before I start cotting it up, and consider 12 cottages to be excellent - suitable for academy for example.
Rostov: gem mine, plains cow, and another food. Could easily be working 10 cottages, but OTOH could be working mines and workshops as well. One way or another, off with the jungle and drop some improvements there - be those workshops or cottages. As you already have mature cottages and commerce buildings (library, market, bank, building university), I guess cot up the rest of it too.
Yaroslavl': building wealth? Either build a building or a unit - wealth only if you're in dire straits with the economy. The city has commerce buildings, and looks extremely cottable. However, it only has one cottage as of yet, so watermills and workshops are still an option. Jungle crew needed here as well - clear the unhealthy foliage and drop some improvements in there.
Yekaterinburg: wait for rep parts, then lumbermills up. Farm over the grassland town, workshop to plains town. It's not going to get any real commerce going ever, so no point in trying. It should stagnate after one point of growth, as working the coastal tiles does not produce hammers. Harbor done next turn, after that it just needs barracks, then it should be producing units and only units (factory + coal plant inserted when needed). It will never reach happy cap, and with harbor doubling fish + clam health it will never reach health cap either.
Yakutsk: I'm not sure what to do with this one. Overall, it looks "mostly harmless", never going to produce serious commerce nor serious hammers. If it can't be a commerce city, then throw barracks in and slowly produce some units. Cities like this often end up working defensive units for me.
Vladivostok: after workboat, you need lighthouse, granary and library. Cottages to the plains and grassland it has, going to work coastal (never ocean - those are useless) tiles + horse + fish + two cots, stagnate by running two scientists. Whip what you need, but the horse provides nice hammers for it to build some part of the infrastructure (whipping is easy with the fish when netted).
Smolensk: like Vladivostok, not going to be much of a city. I guess the desert iron mine can be shared with Yakutsk (if Yakutsk is to produce units, it could use that for hammers). Smolensk can work some coastal tiles, but the food surplus allows nicely hiring two scientists. Library up as soon as possible, with the food you have whip all buildings you need.
Philadelphia: generally what is under the jungle is cottages

Philly however is under cultural pressure and overlaps with cities in all directions. Just cottage whatever tiles it has left after those major cities have theirs. Artist is a good choice to work for as long as the cultural pressure persists (AI is bad at managing cultural borders, so you should be able to press the borders enough for philly to claim it's fat cross worth of tiles from the south), then switch over to scientists as food allows.
Orenburg has enough food to work five specialists. Either by caste system or simply by having buildings that allow it to run specialists. This could net you a fair amount of gold if you build market and grocer (2 merchants each was it?), or nice beakers if you run caste system. Five specialists means that you have to make choices regarding which types you're running, as they will be producing more great people points than other cities, thus netting your GPs. Oh yes - citizen specilists are simply useless. One hammer? Oh dear... crack the whip to get some infrastructure so you can run real specialists instead, or switch over to caste system.
.. at this point I checked it, and looks like you're running mercantilism. That explains the useless citizen specialist.
Edo: assuming it can at some point claim its fat cross, it definitelly could be cotted up. And it did come with Academy, so that might even be preferable. Still, I'm not sure if you have enough production cities, and Edo could become one with mines, watermills and workshops.
Moscow does not have a single cottage, but the terrain doesn't really lend for superior production either. Exactly the type of capitol that drives me nuts: commerce? Not truly cottable. Production? Not really superior. In this case I guess farm one grass (chop forest) so you can work the plains hill - and mine it. Moscow will get a nice production boost eventually from biology and another from state property, those two together allowing some workshops to be worked.
St Pete has good production potential (still some hills to be mined), so I'd rather farm the grass than cot it, then work more mines.
Novgorod: when you get rep parts and lumbermills, this will be a strong production city. Cottages are thus not needed, as it won't break 40 base commerce barrier ever - not even 20.
I think you'll need three production cities to produce reasonable amount of units to continue full war for real.