Two questions here, one editing related and one gameplay related.

1) How many tiles in a prospective city's radius need to be "useless" (ocean, desert, mountains) before you consider a particular city placement to be not worth the hassle, given an otherwise decent city? How many before you would try to move one tile sideways and lose a benefit (resource, river, coast)?

2) How can I edit the minimum distance between cities?

2) i don't know. you can settle two tiles away if the cities are on different land masses, so maybe you can tweak that somehow, but hopefully somebody who really knows will come along rather than me just stabbing in the dark.

even 1) is really variable for me. i love big happy healthy cities, more than i ought to. but i've calmed down about it somewhat, and now i realize that it's going to be quite a long time before a city has people working all 20 tiles. even when it hits 20 population they may not all be out working the fields, i might be running some as specialists by choice and not necessity. so i don't freak out about 3 or 4 any more, or even more. i really hate to see useless desert in my capital but sometimes i just sigh and take a couple junk tiles even in my capital just because it's really the best choice in the situation. in those cases i definitely have to take a deep breath first, and remind myself that i can always move my Palace later ;).

the purpose i have in mind for each city completely determines what makes it "decent". if it's there to block off land to let me backfill later, it can be pretty darn trashy. today i settled some 100% junky ones, but i was in the last 15ish turns of a domination win and i had plenty of food and hammers available due to corporations so it really didn't matter what tiles were near a city; it could be self-supporting even if all the tiles were peaks/deserts probably. expensive, but self-supporting for food/hammers.

that's entirely different than 2000 BC when you have to worry about distance costs since you don't yet have ways to make money or keep your costs down, but you also have to get strategic resources or else. often i overlap a food tile in my first city on high difficulty levels. like pigs for example. keeps maintenance costs down, which are more painful, and i get use out of the improved tile all the time. then again i have the patience to swap around which city the tiles are assigned to, not everybody does.

i guess my main point, if i do have one, is: if you're trying to figure out what sort of city overlap works best for your style and/or how many wasted tiles you can afford, pay attention in a big-picture sense to how long it takes for you to use all the tiles in your city crosses. you might be surprised by how long those sub-par tiles really don't matter since you don't have the population for them anyway. then again, you might not be nearly as new as i'm assuming by typing that, and if so i apologize! somebody referred to me as "in teacher mode" earlier today and i suppose that's true. so no offense meant.

2) will have to wait for a modding-expert.

1) greatly depends on the "benefit"
For example a fresh water bonus is small and can be compensated by a harbour, ozean tiles can be compensated by trade routes... and a ressource may justify a junk city whose sole purpose is to claim it (I want my Civ3 colonies back :mad: )

There is also a difference between completely usless tiles (desert, peak) and marginal tiles (ozeans), I don't count the tiles but rather the raw-potential of the future site.

In a recent game I founded a city that almost all desert, with one rice paddy and one oasis. The reason? Strategic location. It was purely to box in my neighbor. It also had an incense square, so it produced a small amount of commerce. The city cost me money, but was basically like a forward military base.

So the answer to (1) varies greatly depending on what you have in mind for the proposed city.