When I lived in Kyoto, I had similar expenses...
Housing:
- 400$/month for a 15 square meter studio next to Kyoto University
- $500/month for a 90 square meter house shared between with one other person (so total price would have been $1000/month south of Kyoto's train station in a poor area)
Health insurance, pension was the same (but a big part of that was paid by my employer)... It's possible to get a refund of the pension when you leave japan (you get back about 40% of what you paid)
Food: same. One thing to note is that the quality of food you can get for around $8 is amazingly high... It's very hard to find restaurants as tasty for this price in Shanghai or Malaysia where I've lived since... I really miss living in Japan for that.
On the wage for programmers, on the contrary to japanese, foreigners have more leeway when it comes to negotiating salary. A friend of mine, worked in a game company and managed to get a 70% raise when he told them he would be leaving otherwise (it was a rather big game company who usually goes by the $100 x year of age + bonus if married rule for compensation)
I now live in Shanghai and spend a bit more than when I was living in Japan but mostly due to housing and health insurance
Housing: $720/month for a 110 square meter apartment in Pudong 20 minutes away from the city center by subway line 2 . It's much more confortable than what I used to have in Kyoto, but I'm too hold for 15 square meters apartments...
Food: cheap chinese restaurants cost around $3, western food and japanese food is more around $15... While I love cantonese food, I really don't like Shanghainese food unfortunately, so I usually go to more expensive restaurants.
Health insurance: $420/month for me and my wife (through a private expat health insurance)