For what it's worth.

By Bank of America Check/Debit card works at the following ATMs:

Japan Post/Japan Post Bank ATM
CitiBank ATMs
7-11 ATMs
Shinsei Bank ATMs work with mine and my friend's BofA cards.

Notes:

*Most ATMs have an English function even if they only accept domestic cards. All the above mentioned ATMs have English functions.

*7-11 ATMs require a minimum withdrawal of 10,000 yen increments for international cards. My domestic ATM cards can withdrawal at 1000 yen increments.
All other ATMs you can withdrawal at 1000 yen increments.

4 digit pins work fine, my card has no fancy chips on it.

Cash is still king in Japan. McDonalds does not accept credit cards, of the convenience store chains Lawsons is the only place I have experience using a foreign card at.

I use cards to cover the major stuff like department store purchases, hotel payment and long distance train tickets.
Almost everything else like small purchases I use cash.