Couple o' comments.
Troy is not now a port but there seems to be a general agreement these days that back in the bronze age it was on a bay. It's bay simply silted up the same way that the bay at Miletus did. Map and details.....
http://www.udel.edu/PR/UDaily/2003/troy030303.html
Regarding historicity of Troy, I don't see how it can be said that the traditional site of Troy (Hisarlik) is proven to be that city. There is an awful lot of circumstantial evidence though that points in that direction. To dismiss it as all myth is off the mark. The Hittite archives refer often to 'Taruisa' and 'Wilusa' and those are generally conceded to be in NW Anatolia (why there was ever any debate there is beyond me). Homer refers to 'Troy' and 'Ilios' (archaic form: Wilios). It is not clear from Homer or Hittites though which was city and which was the country or if the were just interchangeable.
Hittite records also refer to a king of Wilusa named Alekshandush who had a treaty with Hittite king Muwatallis. Greek legend calls Paris, 'Alexandros' and an obscure legend has him meeting a king 'Motylos' when first arriving in Anatolia after abducting Helen. Alexandros,Wilios,Motylos and Alekshandush,Wilusa,Muwatallis... too many coincidences, I think, between legend and archives for this stuff to be simple fabrication.
Well, if you are still awake, how is this mod fixed for maps and cities? Are you using the Eratosthenes map or the 'Hellas' map of Greece and W. Anatolia. I had worked on a version of the Hellas map for a while making minor corrections and putting in cities/civs for the Trojan war period. Civs included "Akhaia" (Mycenae/Sparta lumped with other 'kingdoms' that would have been subject - or probably so), Knossos, Ithaka, Pylos... etc, major, independent Greek kingdoms. Also allies of Troy... Phrygians, Thracians, Lycians, Maeonians, Amazons (!!) etc. Very difficult finding cities for the period esp. outside Greece and it is a hodge-podge of legendary, bronze age, classical and modern names(that
were bronze age sites tho). Xen is probably cringing but I believe it is the best that can be done with the present state of knowledge. My Phrygians frankly border on wishful thinking but I think everyone else is on much more solid ground. If you are interested and someone can tell me the procedure for attaching a zipped map, I will do that. At least I think it would be useful for info if not usable "as is".