I visited Japan for the first time March 13-28 2019, here are some general notes from the trip.
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Trip duration: I walked a lot (sometimes 19 km/day for several days) up and down hills, to and from train stations; this was tiring enough that it was a mistake to stay for 14 days; I should not have stayed for longer than 9-10 days; this would have saved money on the JR pass (7 days instead of 14 days) and hotels.
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https://www.jalan.net/ seemed to have the best prices and largest selection of hotels. Book at least two months early for good+inexpensive options.
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I did not have a problem with smoke in any of my non-smoking hotel rooms in Henn na Hotel Tokyo Akasaka (100% non-smoking), Hotel IL Verde Kyoto, Hotel Intergate Hiroshima, Hotel Trend Kanazawa Ekimae, or Fudo-in in Koyasan.
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There are a lot of smokers (sometimes in areas where it is forbidden to smoke), but their smoke was never a real problem for me.
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Bike rentals generally require some registration process with a lot of fields, so if you wish to bike around anywhere, this is worth figuring out before arriving.
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Once in Japan, ALWAYS WATCH YOUR STEP especially if you're used to ADA-regulated public spaces: Japan has inconsistent step heights, steps made of out of random stones, steps that are barely visible when going down, sidewalks with a barely-visible height change from the street, surprise obstructions for you to trip on, and ditches to fall into. I twisted my foot in Atami on the first day on a sidewalk and mostly recovered, but you may be less fortunate.
If you do not WATCH YOUR STEP and trip or twist your foot, your wonderful vacation may end very early.
The Japanese are so used to these hazards that they seem to go unnoticed.
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Remember to LOOK RIGHT before crossing.
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People can't seem to walk on just the left side of a sidewalk, but you will generally win the game of walking-into-each-other chicken by staying on the left side.
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Carry enough yen everywhere because almost all of the cheaper tourist attractions, shops, and stalls cannot charge credit, debit, or IC cards.
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Unless you perversely enjoy it, don't carry your backpack as you explore, take a small messenger bag with your drink / SIM cards / charger / power bank.
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People who do transactions with tourists almost always know enough English to do transactions, although it will sometimes be more laborious for them to deal with you. If you have problems, repeat key words, point to things, speak with short pauses between words, or type into Google Translate.
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Your experience will be very different if you are conversationally fluent in Japanese. You need Japanese to get into some places and to talk to the majority of people, who have no interest in English. Japanese learners grinding kanji/vocab/phonetics may want to actually do the immersion needed to get fluent. I have not managed to.
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Google Maps seems to know about half the businesses that exist here at best. Many 7-Elevens are unlisted. Wander into a shopping area and Google Maps will sometimes know about just a small fraction of its stores. I also encountered a bus stop (in Ginza) and a hotel (in Kanazawa) being displayed in the wrong location. You may sometimes need to do a Google Search and hopefully find more accurate coordinates.
Bring a portable power bank for your phone or you will (like me) be awkwardly charging your phone in a 7-Eleven after a long day. iPhone 8 Plus seems to last for about 6 hours of usage at max brightness using Google Maps, taking photos and video, and some browsing. If you wish to record a lot of video, bring a power bank that can do at least two full charges.
I ordered an 18 day Unlimited SIM Card from japanwifibuddy a week in advance. This was the only vendor I found with "unlimited" (3+ GB/day) on DoCoMo, which supposedly has the widest coverage in Japan. japanwifibuddy shipped three 6-day SIM cards to the post office in Narita Terminal 1. Because my flight was delayed, I was only an hour away from missing the 20:00 post office closure, so consider having japanwifibuddy ship to your hotel. The post office was a long walk from the arrival gates, but the SIM cards worked fine on an unlocked iPhone, even without entering APN settings. Setting up a hotspot required entering the provided APN settings.
Take your SIM removal tool with you, one is not provided unless you pay more.
The only times I had no signal with were inside train tunnels and in the forest east of Nara Park. The service was otherwise very good, even inside stations and trains.
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A JR pass is activated on a certain day and expires at midnight after 7/14/21 consecutive days; do not think that you can still use the pass +7/14/21 days later because it has already expired then.
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If landing in Narita, the Narita Express isn't fast or interesting enough to be worth burning the first day of the JR pass on, just take a slightly slower bus or train. I had no problems with the Tokyo Shuttle bus when returning to Narita.
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Taxis are available but 2-3x more expensive than Uber in the US.
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If you have a JR pass, you need to present it to the manned booth when you enter and exit a JR area; this booth is to the left or right side of the IC faregates. People walk in both directions by the manned both, do not be afraid to against traffic. At Tokyo Station, this is confusingly a large enclosed booth.
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If you do not have a Suica or Pasmo card, get one as soon as possible to take the local trains. If you're getting a Suica, only the black Suica machine can give you a new Suica card. If you have a wallet with an outer pocket, this is a good place to keep these NFC cards so that you can just swipe your wallet on the readers.
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Most cars are reserved-only on a shinkansen, if you have no reservation but get into the wrong end of the train, you may have to walk a long way to get into a non-reserved car.
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You can make seat reservations at a JR ticket office for no additional charge.
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Some trains are reserved-only.
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JR doesn't go to Koyasan, you need to take a Nankai train to get there, not covered by the JR pass.
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Nankai's Koya Limited Express gets to Koyasan faster by skipping stations. The seats on the express train are reserved-only. If you want this train, you pay for non-express portion with your IC card and the express portion with an extra ticket from the machine at a Nankai station.
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This station is very large, confusing, and busy. Not the ideal place to first arrive if you can avoid it.
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If you failed to get yen at the airport, there is an international ATM machine on the first floor that you can use to withdraw yen: http://www.tokyostationcity.com/en/information/atm.html
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7-Eleven stores have international ATMs that you can use to withdraw yen using your debit card.
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Assuming your international withdrawal fee is low, you will get more yen for your dollar with an international ATM than the currency exchange places.
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Call your debit card issuer and put a travel notice on your card before your trip.
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Write down your PIN somewhere unless you use it all the time - you may be too tired to remember anything.
Tokyo is enormous and feels like dozens of cities glued together. You could spend all of your time here and probably not regret it. Staying in just Tokyo, you save money by skipping the JR pass and save time transporting yourself around the country to many hotels.
Even with all the tourists, Tokyo appears to be 99% Japanese when outside major tourist traps like the Nakamise Shopping Street (very crowded) in Asakusa.
University of Tokyo is interesting to walk around in as an escape from all the touristy areas.
Tokyo Skytree during the day was more interesting than Tokyo Metropolitan Government Building at night, but I feel like both were worth visiting.
Interesting and much less crowded than Tokyo. Cosmo Clock 21 was worth riding. The engine room of the Hikawa Maru was fun to look around in.
If you are taking the shinkansen here from Tokyo, sit by a right-side window for a possibly-fantastic view of Mount Fuji apparently floating in the sky.
Kyoto Tower is interesting to look from and not very expensive.
Compared to Tokyo, Kyoto appears to be a sprawling low-density mess, but that's just the city center; the interesting places are on the outskirts, and unfortunately far apart from each other. Consider taking a look at a map and planning your itinerary in advance here.
Arashiyama Bamboo Grove was nice and had very few people at 7am.
Iwatayama Monkey Park was a long hike up, and the monkeys were nice but not especially interesting because I had seen them on YouTube so many times before. The hike here does take you up Arashiyama to a nice view of Kyoto, but there are several other places to get a good view of Kyoto.
The Higashiyama Hanatouro was the highlight of my visit here. The path went through several temples, one of which had a pitch-black enlightenment cave/maze/tunnel.
Chinese tourists absolutely love Nara Park. The deer are hungry for deer crackers and may be aggressive once they see that you have them. They'll also eat just about anything else, including bits of paper.
The deer defecate everywhere (they are not like alpaca), don't come here in your unprotected sneakers because removing deer crap from your shoes is not so fun.
I wandered off into the forest east of Nara Park without realizing it was quite uninhabited. There are two bathrooms on the trail (only one of which has electricity - don't assume you'll be able to charge in the other one), no DoCoMo coverage for much of the trail, and mostly very quiet. I encountered two tanuki here who ran into me on top of a hill. I was alone and quite happy to make it out before sunset. Don't be me, don't wander off into the forest alone.
Okunoin Cemetery was my favorite destination during this entire trip. It is enormous, with thousands of statues. Okunoin Temple and nearby buildings were also very interesting. If you are already busy going around Japan, I would not miss Koyasan.
You'll need the bus here to go east-west around town. Read the bus instructions!! Take the ticket when you enter and pay at your destination. The bus driver needs to count your yen before you drop them in.
Arrive here 3 hours before sunset to have adequate time to find your hotel and then go straight to the cemetery in the evening, when it is quiet and perfect for photography. Come again in the morning and watch the sun shine through the forest. There is a lot more activity in the morning, as workers try to fit in new gravestones, perform repairs, and clean up the cemetery.
The monks at Fudo-in were nice, their shojin ryori meals were good, and the morning service was interesting. But side-sleeping on a futon on a floor was impossible. If I come to Koyasan again, I would stay in a hotel with a mattress. If you wish to try shojin ryori (or other styles of cooking), you can do so elsewhere, unbundled from the futon-floor arrangement.
Kongobuji Temple was worth visiting to learn a bit about how Kūkai founded Shingon Buddhism. Photography of the panels was not permitted, you'll have to look at them yourself.
I looked through Hiroshima Castle, but it didn't really interest me.
You might be able to see some tennis games and cheerleading going on at the nearby Hiroshima City Central Tennis Courts.
The atomic bomb museums and memorials here are very moving. These take about a day to look at and were very much worth visiting.
Absolutely packed with Japanese tourists. Lots of vendors with edible food and omiyage.
The deer here do not get fed deer crackers and will not bother you, unlike those in Nara.
I walked around town and then spent the rest of the day going up the Miyajima Ropeway and doing the short hike to Mt. Misen. Visibility wasn't particularly good, but I assume this varies greatly.
It felt cold and wet in March. I took a local train to Uchinada (320 yen one-way; Suica/Pasmo not accepted) and watched a glorious sunset. I didn't have a chance to look at much here because I could not do any more walking.
Photos https://photos.app.goo.gl/GTkeJbzRNLDn2bNm9