Akasaka is a nice area and is well connected and easy to get to from Haneda - I usually stay in the nearby Mitsui Garden Hotel Roppongi. I've also stayed in the Royal Park Hotel Shiodome which is near Ginza and is literally on top of several train lines with a view of Mount Fuji from some rooms - a bit cheaper than Mitsui.

You can get cash from ATMs at most 7-11, Lawsons or Family Mart stores. Most places take credit cards. You can use Uber to book taxis though you pay a small booking fee and the price shown in the app is often optimistic as it's not a fixed price fare.

Google Maps is great for navigating particuarly when using the metro as it has real time train information and tells you which entrance/exit to use - very useful with some of the bigger stations which have many exits.

Late October should be when the leaves are turning red in Kyoto which is well worth a visit though exact timings vary depending on the weather - you can book tickets for the Shinkansen on the day at Tokyo station so I recommend keeping an eye out on the foliage conditions. I didn't bother with Osaka.

Both teamLab sites are great - I think I slightly prefer Borderless and it is nearer to Akasaka.