I never really stopped to figure that maybe it was just foreign stuff that was crazy expensive. One of the really eye opening things I've learned in the last few years is how relatively affordable housing can be...even within the Tokyo city limits. https://www.youtube.com/watch?v=iGbC5j4pG9w -- older homes can be much much cheaper.
Here's a $1600/mo house https://www.youtube.com/watch?v=As2XMhqNBx8
This needs to be considered against local incomes of course, so they're a bit less tempting to locals than to American foreigners from ultra expensive coastal cities.
Part of this seems to be the particular Japanese combination of the shrinking and aging population + continued attempts at maintaining GDP via construction works + cultural preference for new living arrangements instead of old construction. But like anyplace, you pay for where you live and there are certainly incredibly expensive places to live.
Outside of living arrangements, public transport, food, clothes, and so on...everything except for personal vehicles is relatively affordable on a foreigner's salary.
However, salaries in Japan are surprisingly (sometimes shockingly low). I think I've heard that a person working in a regular "salaryman" job can expect to earn around their age * 10,000 USD. So if you're 30, you'll make around $30k USD. This information is a bit old, so expect it to be a little higher, but this table [1] from 2014 suggests a 32.4 year old computer programmer makes an average of 4,256,000 yen per year..or about $38k. Some occupations can make significantly more...but it's interesting to find yourself on this table and consider it.
1 - http://nbakki.hatenablog.com/entry/Annual_Salary_by_Occupati...