What I've been doing is taking about JPY20,000 at a time out from a 7-11 or Lawson ATM (foreign bank friendly machines) and using it here and there as I go, and then all of the excess cash, save for maybe 1,000 is given to the hotel at check-out as partial payment against the final bill, with the balance going to my credit card. That way I never need to worry about orphan currency.

It's better to take out more than you really think you need and deal with the excess this way rather than continually visiting the ATM and racking up bank fees.