Dear Sqhype,
I am not a too frequent visitor here but I love my Civ. Let me try and give some input to your MOD in relation to Bosnia. I saw the discussions on the Bosnia and Herz. Civ Mod but a lot of it is just not with the best intentions.
You are also wrong to state that the Bosnians are Illyrians originally. Clear evidence of this is the "Bosancica", language used in medeavel Bosnia which is Slavic.The Bosnians are South Slavs, just as are Croats and Serbs. Just as those tow, the Bosnians formed their own kingdom at around 1080. Stjepan Tvrtko (not Stefan) is one of the Kings of Bosnia. In 1463, Ottomans conquered Bosnia which later became a pashaluk or ejalet, one of the provinces in the Ott. Empire.
In the period from 1080 to 1463 there was a special kind of church in Bosnia, the Bosnian Church or the Bogumili, related to Bulgarian manicheism. This church was not very well organized and the King remained catholic under the Hungarian and Papal pressure. With the arrival of Ottomans, Serbian Orthodox Church gained ground, but it was mainly the Islam that had replaced the Bosnian Church. It will be interesting if you can replay this in your MOD/Scenario.
As a conclusion, Bosnian, Croatian and Serbian kingdoms were all separate kingdoms at the time. Only with the rise of nationalism in the 19th century did the political and national influences come to Bosnia from its neighbours, culminating in the 1990s wars. Anyway, enough about history, let's enjoy your mod, here is some more useful info for you:
Flag: Yes, it is corect to use the Fleur-de-lis seal, that was the symbol at that time.
Cities: Vrhbosna as the capital (Renamed Sarajevo after the Arrival of the Ottomans)
Travnik (was a royal city at some time as well)
Jajce (this is where the last Bosnian King was beheaded by the Ottomans)
Tuzla
Banja Luka
Zenica
Bobovac (Old Royal city)
Vranduk
Visegrad
Foca
Visoko
Bugojno
As to the special unit, the Knights were the most powerful at the time. Bosnia has a lot of mountains, so some extra movement to its knight or maceman may be useful. Also to meet the Ottomans in Kosovo polje. Bosnia had a great relationship with Ragusa (today's Dubrovnik) and a nervous one with Hungary and the pope. They were ok with the Serbs and the Byzantines, but were under the pressure from there as well.
I hope this is useful...