3-4 days in Tokyo is a great plan. Start with my 2 Days in Tokyo post to see my top recommendations. If you’re in Tokyo in May, September, or December get tickets to a sumo match. I found Tsukiji Fish Market very interesting and thoroughly enjoyed the tuna auction despite the 3am wake up call.
There is a lot to see in Kyoto and it can easily take several days to see and do everything on your wish list. That said, I also highly recommend taking day trips outside of Kyoto to experience other regions of Japan.
Take a day trip from Kyoto to Hiroshima (about an hour by bullet train) and see the Peace Memorial Park, which was created with the sole purpose of encouraging peace between nations. Kyoto is also super close to Nara, where you can see the world’s largest wooden building and feed tame deer, and Kobe, an international port city with spectacular night views from the Shin-Kobe Ropeway.
During your time in Kyoto, I recommend staying at least one night in a ryokan (a traditional Japanese Inn). They can be pricey, but keep in mind the price usually includes a kaiseki (traditional multi-course Japanese meal).
The only months you can really climb Fujisan are July and August, but there are lots of places to go for amazing views of Fuji. Hakone is a scenic mountainous region about two hours from Tokyo by train. In Hakone, the Hakone Open Air Museum hugely exceeded my expectations. It’s one part museum, one part park with interactive structures for kids and adults and a very cool indoor Picasso exhibit. The old world ships that cross Lake Ashi have fabulous views of Fuji (unfortunately when we were there it was incredibly foggy and we couldn’t see Mount Fuji or take the lake cruise). Hakone is also a great spot to soak in an onsen (Japanese natural hot springs). Because there’s so much to do, Hakone is a common overnight destination.
The Japan Rail Pass is a fantastic deal for tourists. You can buy the Japan Rail Pass here.
You have to buy the pass outside of Japan, but it will save you lots of money if you plan on going to more than one city in Japan.
In the major Japanese cities you will find English speakers, but you’ll still likely have communication difficulties. Most restaurants have menus in English, but some restaurants have menus only in kanji (Japanese characters) (that’s when you get to point at the menu and hope for the best).
There are Japan transit maps in English and Hyperdia.com is a great website for determining train times and costs throughout Japan. I also recommend using the app Tokyo Rail Map Lite.
Tokyo is a very walkable city! Randomly wandering around the city is a great way to find tiny hidden shrines and delicious hole-in-the-wall ramen joints.
Do you prefer to wander randomly through new cities you visit or do you like to have a sightseeing plan?