When I last went I exchanged cash at my bank for yen before I left. I brought $500 USD equivalent and needed $100 more. Luckily my hotel had a machine with no fees and I had a few hundred USD. I would plan on a lot of cash.
I agree, after thinking about it more and seeing all that wasted time on a bus I am going to go solo. Like you I am using their itinerary as a starting point.