How to Rename Regions
Renaming regions is simple if you know the file structure of the game. All you do is go to the folder of the region you want to rename, and look for a text file (it should be a sheet of paper with a gear or cog on it). Open that text file, and you should see something like this:

[Regional Settings]
Name = New York
Terrain type = 0
Water Min = 60
Water Max = 100

So say if I wanted to rename New York "Old York" I would replace New York under the name column with "Old York" to make this:

[Regional Settings]
Name = Old York
Terrain type = 0
Water Min = 60
Water Max = 100.

If you go into the game, you should end up at the Timbuktu starter region, and in the load regions list, you should see Old York! Congratulations! You renamed your region!

How to Rename Cities
Renaming cities can be done from within that city you want to rename. Simply load the city you want to rename, press Ctrl+X. This will open the cheat input panel. Simply type in WhereRUFrom [city name] So say for example if I wanted to rename Pleasantville "Unpleasantville" I would type in WhereRUFrom Unpleasantville.
Keep in mind that in names with 2 words, you cannot use spaces, otherwise it will not work. Instead you will have to use an underscore. (_)