For Part 1 click here.
Day 11: Pit Stop in Nara

Giant Buddha in Todai-ji temple (c) ABR 2017
It’s quite a journey from Miyajima to Nara (around 4 hours if you catch the right trains; could be a bit longer if you end up on a local train from Kyoto), but there are some special sites here that make the travel time worth it.
Todai-ji is one of my favorite shrines/temples in Japan (which is really saying something, because I have been to a lot of them). It houses a massive, beautiful Buddha statue, and hosts a healthy population of Nara deer as well (the town’s mascot). I have three pieces of advice for this area. (1) Make a point to visit the temple; it is a work of art. (2) Stop by Buddha’s “nostril,” a little hole in a giant, wooden support beam of the temple, and see if anyone tries to climb through. The experience is said to grant a bit of enlightenment, but it looked far too small for me to try (and most other people). But a few kids went through and it was adorable. (3) Please DON’T feed the deer, for your safety. The first time I visited, I bought some food for them at a shop and they bit my legs as soon as they saw I had something. Not worth it.

A Nara deer (c) ABR 2017
Yagyu Kaido is also accessible from Nara, and although I have not gone myself, it looks to be a great place to hike through one of the older forests on Japan. I would suggest staying an extra day if you’d like to give this a sufficient amount of time, however, because the trip from Nara to Nikko is considerable and the temple deserves at least an afternoon/morning to explore, if not more.
Day 12: Survive the Train to Nikko
Today shall be a day of trains, so I’ll add a few tips on finding food and keeping your sanity during train travel days in Japan.
First, when it comes to seating, I would highly suggest that you reserve yourself a seat on the shinkansens. This may mean that you have to wait a bit, but the non-reserved cars tend to be more crowded. Reserving a seat is free with a JR pass, is done the day-of at the JR station, and may allow you to sit next to your travel partner(s) if you have them.
For food, there is no lack of snacks inside the train terminals, but if you aren’t a fan of cold bento boxes and convenience store food (or just get tired of them), your best bet for a good meal is outside of the ticket booths. In the big cities, like Kyoto and Tokyo, you are likely to be near a department store, with lots of options, and many of the smaller stations with shinkansen stops have somewhere to get a hot meal.

The red bridge in Nikko (c) ABR 2017
Anyway, in order to make it from Nara to Nikko, you will need to take a train back to Kyoto, and then take a Shinkansen to Tokyo, and another from Tokyo to Utsunomiya, and finally the special train from there to Nikko. All of this in included on the JR pass.
Suggestion for accommodations: Minshuku Narusawa Lodge – the owner will pick you up from the train station and help get you oriented. There is also a nightly trip to an onsen (for extra cost, but very enjoyable).
Day 13: Temples, Temples, Temples, Oh My!

Some crowds among the temples (c) ABR 2017
Today is the day to explore Nikko’s many temples! According to UNESCO, there are 103 religious buildings in Nikko, and when you get there, you won’t doubt that number. From the lodge (if that’s where you stay), it is about a 30 minute walk up to the area, but I would suggest getting two-day bus pass down at the JR train station. This will be handy today and tomorrow, and get you all around town; there is a ton to see, so you don’t want to waste too much time walking between sites.
I have two favorite places to visit in the complex itself. Tosho-gu is a Shinto shrine dedicated to the major Japanese historical figure, Tokugawa Ieyasu. It was VERY busy when we went there the last time, but the intricacy and vibrant paintings/carvings of this shrine are well worth the hordes of children and tour groups that you may need to brave.
After the swarms of people, my personal favorite spot in this area is a short hike north of the main complex to a set of three small shrines along a creek. There aren’t many people that come here (due to the walk and its relatively small size), so I have found this place to be extremely peaceful and more spiritual than almost anywhere else that I have been. I’m not going to just throw the name at you though, because I’d hate to see people crowd this area. If you are really interested, you will be able to find it on a map of the complex. The hike is only 15 minutes or so from Tosho-go, to the north.

The many Jizo along the river (c) ABR 2017
After you’ve had your fill of temples and shrines for the day, walk over to Kamangafuchi gorge to take in the powerful beauty of the river as well as the watchful eyes of the 70 Jizo statues that are lovingly clothed with caps and aprons here.
If you’re staying at the lodge, I would highly recommend taking a trip to the onsen tonight. It is affordable, friendly to foreigners, and a must-do, cultural experience for Japan. (But you will be bathing naked with strangers, so be mentally prepared and go with an open mind).
Day 14: Up Into the Clouds at Mt. Nantai

The steep trail up Mt. Nantai (c) ABR 2017
If you are a hiker, I would suggest that you wake up early today and take the bus up to Mt. Nantai. This is a serious, uphill trek, and if you want to hit this, get as much of a mountaineering start as you can. This also is not as developed as Mt Fuji, so expect more along the lines of US trails in terms of bathrooms (ie there aren’t many). Also, please be aware that this trail is pretty undeveloped and rugged; I would only suggest this if you are in shape and have experience on the mountain. Even if you don’t have time for the hike or don’t want to risk it, be sure to visit the shrine at the bottom of the mountain and send up good thoughts/prayers to the mountain spirits.

Kegon falls (c) ABR 2017
Mt Nantai is also near a lovely lake, a waterfall, and plenty of food. So, we made a day of it when we went up here. Afterwards, we tuckered ourselves out by taking the train all the way over to Sendai (Nikko-Utsunomiya-Sendai).
Day 15: Restful Urban-cation in Sendai

Zuihoden (c) ABR 2017
After all that you have done, take a day in Sendai to get some rest. There are a few little things to do here, but we’ll get to the best attraction tomorrow. If you get antsy, go check out the giant statue of Sendai Daikannon. It is the 6th largest statue in the world, and absolutely beautiful. There is also Zuihoden Mausoleum, but I would prioritize the statue, because it is unlike anything else you have done so far in the Japan (if you follow this itinerary).
Day 16: Temple of the Mountains in Yama-dera

Temples in the mountains at Yama-dera (c) ABR 2017
Yama-dera is the best attraction in the area near Sendai, and if you ask anyone about what to see while you are there, this is the place that will pop up. It is about 1.5 hours on a JR train over to Yama-dera. Once you arrive, you will take a stroll through the small village at the base of the mountain. If you are going to need some energy in order to climb up 1,015 steps, stop by one of the restaurants here and grab some grub.
Otherwise, follow the signs to the base of the staircase, and purchase your ticket for the temple, then get huffing up the hundreds of steps. Luckily, the struggle is worth it for the beautiful views of the valley, and opportunity to visit some of amazing shrines that are perched on the edge of the mountain cliffs. There’s no better reward for making up a steep incline than all this Japanese beauty (except ice cream, which you can get when you get back down).
After this, take the afternoon to get back to Tokyo. That will involve taking the train back to Sendai, and then a shinkansen back to Japan’s capital.
Day 17+: Exploring the Urban Jungle of Tokyo

Rainy day in Tokyo (c) ABR 2017
Depending on how much you love cities, gauge how many more days you’d like to spend in Tokyo. If you haven’t see Akihabara, Shinjuku, or Harajuku yet, check them out. Otherwise, you may want to catch a train to one of the surrounding cities. Yokohama has a really cool Chinatown, and Kawasaki is home to one of the most special arcades you will ever see which has a couple floors modeled after Kowloon the Walled City.
Once you are happy with your city experience, head home!