Here's my proposal for the map.
I've re-added a lot of resources in Libya and the Balkans, as well as putting back in the hills and rivers in Serbia and Bulgaria that were removed in your version for some reason. I also basically added in my buffed Libya (perhaps a little too fertile actually), and I reverted Morea to its original shape (it looks better and more like the actual peninsula in my opinion). Regarding the cities, I removed Ragusa (not actually on the map and not really controlled by the Byzantines by this point anyway), Corinth (I thought it crowded the Morea too much, with Athens-Patrae-Mystras all tiles are covered with minimal overlap), Ochryia (Not a very important city, not firmly controlled by the Byzantines, and crowds Thessaloniki) and Heraklion (I thought that a city on Crete was kind of unnecessary, though I suppose you could make a case for it). I also moved Thessaloniki to more accurate position, and I may have moved Dyrrachion (mainly because I removed it, then on further research put it back). I've also added/made Skadar, Skopie, and Plovdivy independent cities to represent Bulgaria and the Serbian principalities. With less cities, the Byzantines will need less of an economic buff (i.e. markets in their cities); preferably their economic situation should be similar to that of vanilla SoI (i.e. slightly losing money at 100% gold at start, but with the means to lift yourself out before too long), I would think. I also reduced the culture of all the cities (except Constantinople) back to 5, which seems to be the standard for preplaced cities.
These are all just suggestions, use whatever you want and think will be best. I'll update the settler and city name maps soon, but given that the changes are rather minor it should be fairly easy.