The easiest places to change money are probably the exchange counters (bureaux de change) at the airports. Most banks only exchange between Japanese yen and US dollars. For other currencies, you may have to place an advance order. It is usually easier to exchange foreign currencies for yen. Not so many places change yen into foreign currencies.
The World Currency Shops in major cities use the same exchange rates as Mitsubishi Tokyo UFJ bank. Most branches are open in the evening, and some even at weekends. See http://www.tokyo-card.co.jp/shop/wcs-shop-e.html.
Major post offices also provide currency exchange.
There is no limit on the amount of any currency that may be brought into or taken out of Japan. However, if you transport any currencies, checks, securities or other monies equivalent to more than 1,000,000 yen into or out of the country, then a customs declaration form must be completed.