OK, so I've been having a bit of a nose around in the editor, so I'll try and help out with city placement. Some areas seem really good, although others are somewhat confusing (like the ancient city of Gordium being in Tunisia). I don't know much about some places, so I'll only post about those which I do
1. India
Mostly spotless, but there are a couple of points I've got
-The city of "m" in South-East India. This could be Pondicherry in real life, perhaps?
-Calcutta did not exist until the British came in the late 17th century. The city of Patna was quite important during this period, and I'd suggest placing it 2 tiles north east of Calcutta (allowing the construction of Calcutta later). I'd also suggest moving Lahore NE one tile, and Delhi either NE one tile as well, or NE one tile, and E along one tile onto where that irrigation is. It doesn't matter that Delhi may interfere with Hyderabad's placement, because:
-Hyderabad (in Pakistan) did not exist until the 18th century. Perhaps rename it Jaipur? or Indore? If it is renamed Indore, it could probably be placed one tile South
2. Siam
-I cannot find the city of Cheju anywhere. Perhaps rename it "Nakhon Si Thammarat"? That was an important city, and is pretty much in the right location
-Saigon should probably go 1 tile South West
-Get rid of Phnon Phen. Replace it with Ayutthaya, the capital of Siam throughout most of the scenario
-Get rid of Bangkok. This would be one tile below Phnon Phen/Ayutthaya, anyway. Rename it "Pegu".
-I'd suggest moving Hanoi North one tile, and NorthWest one tile
-I'm pretty sure Da Nang wasn't really a city until the 17th century, or so
3. China
I don't know much about China's geography, compared to the previous 2, so I probably won't have much in regards to suggestions, etc.
-Taiwan should not have any cities on it at the start of the scenario. It was only brought under the Chinese domain some time in the 1600's
-Fuzhou looks too far North. I'd suggest placing it one tile South and one South-East
-Move Nanjing one tile East, get rid of the city of Nanking, as the two are the same. I'd suggest replacing with the city of Jinan, two tiles NE of where Nanking is.
-Beijing should go two tiles North (or one tile North and one North West if you want to avoid a coastal Beijing).
-Get rid of Tsingtao. This city did not exist until the 1800's. Perhaps replace it with the city of Zhengxian.
4. Japan
-Get rid of Sapporo, the city did not really exist until the 1800's. Don't replace with anything really, just leave the spot for the AI to potentially settle.
-Get rid of Sendai, which was founded about a hundred years after the start of the scenario, replace with Akita
-Same with Nagoya, replace with Edo, one tile East
-Get rid of current Edo, put a city location there for Sendai to be founded later.
-Get rid of Tokyo. This is the same city as Edo. Replace with a spot for Hiroshima (one tile South West, so there is a chance that it does not get engulfed by Kyoto's culture when it expands, because otherwise the AI will never found a city there).
5. Persia
Persia seems to be a mess, filled with ancient cities! Although I know it was like this in the scenario you have based your off of, too

-Get rid of the Ancient city of Persepolis. This is located where Tehran (Safavid capital) should go.
-The current Tehran should be renamed Hamadan
-Move the ancient city of Pasargadae one tile South West, rename Shiraz
-Move Arbela 2 tiles North West, rename Mashhad
-Delete Antioch. Replace with Kabul, 2 tiles South and 1 tile South West (where the hills currently are)
6. Ottomans
Not much to change here.
-Edrine should be moved 2 tiles South East, and be renamed Sanaa
-Cairo should go one tile North
-Historically, Bursa should go 1 tile NW, although I can see why for gameplay reasons, you would not want this.
-Sinop should go one tile NE, and be renamed Trabzon
-Baku should go one tile East, and one North East
7. Scandinavia
-Rename Aarhus in Iceland Reykjavik
-Rename Aarthus in Norway to Stavanger
-Stockholm should go a tile or 2 North
-Malmo should go 2 tiles NW of Kristianstad (you can keep them both in)
-Helsinki should go 1 tile South and one South East
-Vaasa should go 2 tiles south, with the tile it currently occupies being a blank city tile, for Oulu to be founded upon later.
-Remove Norrköping (which is too far North). Replace with Luleå.
-Remove Västerås (which is again too far North). I don't know what- if anything- should go here instead.
8. Barbary Coast
-Only thing here is to get rid of Gordium, and to move Tripoli 2 tile NW.
9. Ethiopia
This one looks like a mess

-Get rid of Intombe (not a city). Replace with Massawa
-Move Axum to where that Forest with a Lion is, 2 tiles North of Addis Ababa
-Get rid of Massaua (which is really the same city as Massawa above). Dunno what to replace it with
-Get rid of Adulis, which is much too far South, and also gone into the sands of time now, IIRC. Rename Mombasa.
-Get rid of Hlobane (not a city). Dunno what to replace with.
10. Mali
-Gao should go roughly where Diffa is, not where it currently resides
-Timbuktu and Jenne should probably swap places, as this is (roughly) closer to where they both reside
-Get rid of Nguigmi. Dunno what to replace with.
-Zinder should go a couple of tiles North, and Tessaoua a couple of tiles North, too (which obviously puts them roughly on the same tile). I would, however, suggest putting the city of Biram on the tile, instead of either.
-Benin City could go one tile SW of where Tessaoua is currently.
I hope this post was helpful. I've got a couple of other suggestions, regarding the Aztecs and Indonesia, and I also need as closer look at some parts of Eastern Europe (and the Golden Horde, which should be renamed the Crimean Khanate, or even the Khanate of Kazan, as the Golden Horde was a couple of centuries earlier)
Overall, looking great

You may want someone with more knowledge of these areas especially, to look over the map, as I do not know enough about them to feel like I'll be helping:
-Kongo (I have no idea of the area, myself)
-Eastern Europe
-Africa in general
-South American, esp. Inca