Could someone post the exact syntax for using the CityList option in the World Builder? I can get them to use the first city name listed but not the others. I must be typing them either in the wrong way or place.

As far as I know, it follows the lists from Civ4CivilizationInfos.xml.

It is possible to override the CivilizationInfos city lists and make one in the Worldbuilder. I think the two examples of this being used are the Crusades scenario for the European Middle Ages mod the the Scenarios section of Civfanatics, or the 1000 AD scenario that came with patch 1.61. I have never done one before, so all I can do is point you to an example.