Use and existing faction and gradually change elements of it - say you've decided you don't want thrace, change names by changing text files so
{thrace} New Roman Faction

then on next stage give thrace the region you want New Roman Faction to have and give their old ones to someone else.

then remove them from owning their old units by changing EDU and EDB files, and assign them new units

then change their banners and logos to what you want for New Roman Faction..


You don't have to do it in that order, just do it in small steps, think of it as adapting existing faction and not introducing new one all in one go, or you're likely to get in a mess!