I too sort of doubt that JET will be too keen on hiring a single parent, but who knows.
Any location away from the big cities will pretty much fit your criteria. Avoid Hokkaido and the mountains, and it will be "warmer" - although I am not sure of what you mean by that. Warmer than what?
Most communities have a preschool (hoikuen) - the nationally run version of kindergarten... But if you want a
private kindergarten you may have to look around for one as they become scarce in the countryside.
The cost of living also drops anywhere outside the major cities. Or, really, outside the prefectures around Tokyo and the immediate area around Osaka. Most of the rest of the country is lower in cost.
I see you posted another thread with similar criteria, so I`ll stick my reply on that one in here too.
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Southern and warmer winters, (don't mind hot summers).
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Most anything south of Tokyo doesn`t get much snow at all. Far south and you get blistering summers.
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Coastal, with access to fresh fish.
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I would be hard pressed to come up with a location in Japan that did not have access to fresh fish. You could live somewhere the furthest from the coast as possible, and still have fresh sashimi grade fish available in every store.
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Isolated or not isolated, town, village.. not a city.
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Be aware that Japanese "cities" are not always "cities" by the commonly understood meaning of the word. It`s a term used for administrative purposes. 50 relatively isolated villages and towns over a huge area can be called a "city". They are just administered as a whole and not individually.
On the other hand, you can have a "town" or "village" that is tiny in size, and crammed literally in the middle of an urban area. It just chose to administer itself rather than joining the city.
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Somewhere in Okinawa (what is a good safe preficture?)
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A better question would be what is an unsafe prefecture. There are very few bad areas in Japan, and the ones I can think of are in Tokyo and Osaka. There really is no such thing as an unsafe prefecture.
Anything in the prefectures around Tokyo risks being urban or at the least very "extended urban / suburban" and not rural.
My personal suggestion would be to look into the mountains, and along the northern coast.