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Currently, what is the average 3 bedroom rental going for in a reasonable distance from the airport?
Rents vary depending on where is it that you want to live, If you decide to live in the Tokyo metropolitan area is going to cost you that first born you are talking about, anywhere from $2,500 to $7,000 USD for a small 2 or 3 bedroom apartment in the most popular areas of the city. Narita is not that expensive and you could get a three bedroom home for around $125,000Y or about $1,500 USD/ Month. $2,000/ Month can get you a fairly decent three bedroom home the further you get from the city center. , a 2,000 square feet three bedroom home in the Tokyo metropolitan area (Shinagawa, Shirokane, Yokohama, Roppongi) will run you $15,000 USD/ Month. I have a small two bedroom apartment (town home style) in Narita (about 500 sf.) and I am paying 70,000Y / Month or about $825 USD.
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Also what are the taxes like?
Since this is a commuting contract and you are not going to get residency status in Japan, you are exempt from Paying taxes in Japan but Uncle Sam will get his cut, if you live in the US and commute from the US, then you are NOT going to be eligible for the foreign residency exemption of your first $94,000 USD (if I,m not mistaken, that is what it is) but you can make quite a bit of deductions with your housing and per diem allowances while you are abroad, consult a tax professional on this matter.
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Also the commutting allowance: is it deposited as part of your paycheck and whatever isn't used is yours, or is it a reimbursement? IE: can the commutting expense be used however I need to use it? IE crashpad etc
You either get the business class ticket or the $2,000 commuting allowance deposited on your pay every month . You also have the option of choosing from month to month the $2,000 or the C class ticket.
Now having said that, your question seem to be geared towards somebody who is thinking about actually living in Japan, I just want to make clear that the company is NOT sponsoring residence visas and that this is a commuting contract ONLY. If you are thinking about living in Japan, you have to arrange residency status by other means (your wife getting an English teaching job, you are married to a Japanese lady, ETC)