Isn't Okinawa a good place to start? You get two interesting comparisons: Okinawans vs other Japanese during the last century, and Okinawans then vs now. It reduces the number (or at least the scale) of differences so that you can better pinpoint the factors, right?
Interestingly enough, Okinawa has the highest life expectancy in Japan. They also really got the short end of the stick during WW2 though (a third of the civilian population died during the US invasion), so this may be a statistical/survival of the fittest type quirk too, plus the historically the local diet there was fairly different to the rest of the Japan (lots of pork, less seafood, sweet potato/taro instead of rice, chillies, bitter melon, etc).
That's because lots of US troops are stationed in Okinawa and with them came lots of fast food chains. Young(er) people in Okinawa eat lots of junk food, and they have shorter life expenctancy than their parents.
