You can try and apply for the Schwab High Yield Investor Checking and Schwab Invest First Visa, which are my personal favorite ATM and credit cards for travel. But I don't know if they'll arrive in time. If not, you'll have them for next time.

If you don't get the Schwab cards in time, the wiki should be able to answer your questions.

1. For ATMs, I'd use BoA for ATM withdrawals over US$175 equivalent (since it's 1% + $5/transaction) and Citi for smaller withdrawals (since it's 3% + $1.50/transaction), with two caveats: (a) if you can use a Citi ATM, the threshold where BoA becomes cheaper increases to US$250 since Citi shouldn't charge the $1.50 (only the 3%), and (b) if you have Premier/Citigold/Private Bank status with either bank, you should be able to get the fees waived.

2. For credit card, if you have the Bloomingdale's Visa from Department Stores National Bank, the wiki says that it's only 1%, so I'd use that. If you just have a non-Visa Bloomingdale's store card, you can leave that at home as it probably won't be any use in Japan. You can also leave your Discover at home, as I don't believe it's accepted in Japan either. The second lowest fee would be your Amex cards (if one is a business card, that will be slightly cheaper to use than a personal card). And bring the BoA credit card as backup in case the others don't work.