How do you mod the mod?

[Atilius]

I always want to play as a single Greek city state, such as Athens or Sparta. So once I edited KH, deprived it of Sparta and Rhodos and their generals and troops, leaving only Athens and change the faction name to Athenai. All goes well until I found that I couldn't save after opening a new game...

That ought to work if you use Sparte rather than Athens. I think the reason this happens is that the CAMPAIGN_SCRIPT.txt script isn't terminating, which prevents you from saving the game. The problem arises because the section of the script that handles assignment of the UnitSize trait expects the KH player to own Sparte. You could fix it for Athens by changing the script to assign the UnitSize trait to an Athenian character, changing "Sparte" to "Athenai" where the GarrisonToPopulationRatio check is being done, and modifying the GarrisonToPopulationRatio values so they're correct for Athens.