Hello,
First, definitely get an IC card when you get into the train station at the airport. It makes taking the train so much easier. During covid and a little afterwards, there was a shortage of chips for the cards so the big cities didn’t have them but the last time I was in you could get them again. If there is an issue, there is an IC card app available for Apple phone users.
If you are staying at hotels or any accommodation that will accept delivery of your luggage, definitely take advantage of Yamato transport to ship your large luggage to and from the airport and to the next city. it is very cheap and makes getting around the crowded trains much easier. If the accommodation doesn’t accept delivery, you can contact Yamato ahead of time with your location and ask if there is a center close by that you can ship it to and pick it up at. Shipping to the airport needs to be done 2-3 days in advance depending on the city.
Pull out cash, in the big cities cards are accepted at a lot of of places but Japan is still a cash country so smaller stores might not accept cards. My rule of thumb is to pull out the max I can at the ATM, there is usually the conversion fee which is a % and a machine fee which is flat. so it is cheaper to take out the max than to pull out a little bit at a time. Then I pay with card whenever it is accepted so I can save my cash for the places that don’t accept card. Generally, you get a better conversion fee when you pay with card so this is the preferred method.
As far as food, go where the locals are going. If you go to the touristy areas, the prices are higher and they will sometimes charge you a table fee. If you need to budget a bit, the grocery stores have cheap, pretty tasty prepped food, even sushi that isn’t half bad.
Make sure you have access to internet. Google maps is great for accurate train timetables and which platforms you need to be on. Download Japanese in the google translate app so you have access to it when you are offline. In the big cities you can sort of get away with English in the very touristy areas but generally the English is limited outside of that and if you get into a situation where your knowledge of Japanese isn’t sufficient, it is useful to be prepared.
In Nara, explore further into the park. The entrance where the deer are is super busy, but if you go further back, the crowd clears out and the walk is quite nice.
In Kyoto, the free temples and shrines are usually packed shoulder to shoulder but there are a bunch of pay for ones (300-600 yen) that are so much more beautiful and far less people
Tokyo is gigantic, plan ahead of time. One of my favorite places to go is Takao-san. Still Tokyo but on the outskirts (3 hours by train) and a nice break from the city. The walk up the mountain to the temple in lovely and the village at the base is very cute.
Have fun!