Prices are dependent on exchange rate which is pretty favorable for us right now. However, who knows what it will be like in a year. Flights - again, that changes often depending on the economy.
Cherry Blosson season in Tokyo is late March / early April and is one of the MOST popular times to visit Japan, so hotels and flights may be at a premium.
Staying at a Ryokan is the least expensive option but is also the least Western. I think the hotel we stayed at is currently running around $200 a night for the same season this year.
I didn't find food to be such a big expense (everyone always says how expensive food is in Japan) but we ate at a lot of smaller places that also were not very Western (but man were they good!).
I don't remember how much train travel was but we didn't buy a pass and did just fine.
Japan is CERTAINLY one of the least expensive foreigh places to travel at the moment. The dollar actually holds some weight against the yen - which is it NOT doing with the pound or euro.
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