japan travel tips

First off, get a JR rail pass, way in advance (they have to mail it to you from, like, France, for some reason): https://www.japan-rail-pass.com/
This gives you unlimited bullet train rides for the duration of the pass (you choose which day to "activate" it once you're in Japan). Very much worth it if you're riding more than 3-4 bullet trains, because those add up quick ($$$). Not that useful in Tokyo itself, since it only applies to JR lines (so all other Tokyo trains will cost extra).

For lodging just about everywhere, I recommend the Toyoko Inn hotel chain (that's To-yoh-ko, not Tokyo):
https://www.toyoko-inn.com/eng/
They have hotels in every major city, free breakfast, laundry facilities if you need them, if you arrive early you can drop your luggage off in the morning and go exploring, rooms are only about ~$70 per night, you can book ahead of time on the English website and see a consolidated list of your itinerary, and they're not shitholes at all. Honestly way less of a headache than trying to cobble together a mix of different independent hotels, imo.

Highlights in Tokyo:
-Jump Shop: As in, official merchandise for Jump series. There's one in Tokyo station, but my favorite is in Suidobashi, right near the Tokyo Dome (baseball stadium).
-Asakusa: big tourist spot. Features the Kaminarimon gate and a big temple. Shouldn't take more than an hour to hit up.
-Akihabara: the one, the only. Multiple 6-story towers filled with figures, games, electronics, arcades, merch of all kinds. Also the place to go for maid cafes (a little squicky but...maybe worth one trip for the novelty).
-Ikebukuro: Akihabara-lite, kind of? Caters more to women otaku/fujo? Still, young and hip but not as greasy as Akiba.
-Harajuku: the place to go to spot crazy fashion. No central attraction per se, but the downhill route from Harajuku down to Shibuya is a nice walk.
-Odaiba: takes multiple trains and a monorail, but worth it. It's a reclaimed land island with a 1/4 scale Statue of Liberty, Rainbow Bridge, Ferris wheel, arcades, shops, etc.
-Yamanote train line: the train that just goes in a giant circle around the entire city. Takes one hour to complete the loop. Fun to just sit, enjoy the AC, and watch the sites go by.
-Izu Oshima: island south of the mainland, accessible by a 2-hour jet ferry ride (yeah, bit of a trek). But practically guaranteed to be free of other (foreign) tourists. The attraction is getting to summit an active volcano (you walk up to the crater rim) at the end of a brutal hike. If you have a day with nothing to do, this is a weird-ass option.
-onsen/sento: not a specific place, but you gotta have the public bathing experience at least once. These can range from little back alley bathhouses (filled with local senior citizens) to giant complexes with food courts, spa services, etc. There's one big chain called Ooedo Onsen that's a safe bet for tourists. Buy big band-aids at a pharmacy if you need to cover up tattoos (though a lot of places won't care because you're obviously not yakuza).

Other places I might recommend, overall:
-Nikko: mountain town north of Tokyo. Known for giant temple complex featuring Tokugawa's gravesite and wild monkeys walking around.
-Kamakura: shrine/temple town, day trip from Tokyo. Famous for the Daibutsu (Giant Buddha). Lotta walking. Very peaceful/scenic.
-Kyoto: The second most important destination besides Tokyo. Very big, very old; lots of tourist stuff to do. Big ones are Kinkakuji (Golden Temple), Gion district (geisha), Kiyomizudera temple, Fushimi Inari shrine (hundreds of orange gates). 2 days is ideal, but you could cram it all into 1 if you're prepared to die. 2.5 hours west of Tokyo (everything's west of Tokyo) on a bullet train.
-Nara: my favorite small city, right next to Kyoto, absolutely worth a visit. Old temples, deer walking in the streets, etc. Could be a day trip from Kyoto.
-Kinosaki Onsen: teeny tiny hot spring town north of Kyoto. Really off the beaten path if you want a break from the big cities. Small canal streets lined with willows, and you walk around in yukata and geta going from onsen to onsen.
-Himeji: 40 minutes west of Kyoto. Known for its giant, well-preserved castle. That's pretty much the only draw. Good, easy stop on your way to Hiroshima, if you're going out that far.
-Hiroshima: 2-ish hours west of Kyoto. You know what Hiroshima's all about. The A-bomb stuff is whatever (sorry), but what I really like is Miyajima island, which is a short ferry ride away. Famous shrine complex (that iconic red gate out in the water) and a cool mountain to hike up. Miyajima also has a combo cat/owl cafe (they're kept separated though).
-Nagasaki: even farther past Hiroshima. Unique, for its heavy European/Christian influence. Cuisine also starts to have that Kyushu flair (I ate whale and horse here).
-Okinawa: I went to Naha (capital city) specifically. Requires a 3-day ferry ride (no thanks) or a 3-hour, cheap plane ride (better). Very very different from mainland, culturally. More tropical/relaxed, with American influences (because military presence).

Places I've never been to but that people like?:
-Ghibli Museum - day trip from Tokyo. Supposed to be great!
-Osaka (close to Kyoto- big modern city)
-Yokohama (close to Tokyo- zero defining features from what I can tell)
-Nagoya (between Tokyo and Kyoto- sounds boring to me, like Kyoto-lite)
-Mt. Fuji (day trip from Tokyo, or on your way out to Kyoto, maybe?)

Food you need to try:
-Coco's Ichiban Curry House: best chain curry around, where you totally customize your order re: ingredients, mix-ins, spiciness-level
-Hamazushi: best chain kaitenzushi (conveyor belt sushi). Stupid cheap, extra tasty, with weird non-sushi items like french fries and cake and duck soba.
-conbini food: each conbini chain has its own line of food, and they're all worth trying. There's sandwiches, noodle bowls, fried chicken, meat buns...
-yakiniku: generic term for grill-your-own-meat place, like korean bbq in the US.
-okonomiyaki: special savory pancake they make for you at your seat. Best eaten in Osaka or Hiroshima (each with their own styles).
-izakaya food: make sure to pick a place with actual cooked food and not just a bowl of peanuts.
-McDonalds: worth trying just once to see the difference.
-Saizeriya, Big Boy, etc.: or any number of the "western-style" family restaurants. Again, just to see their odd take on what *they* think *we* eat.

Other general tips:
-Do not expect anyone to speak English. This ain't Europe. This means a lot more planning ahead of time unless you're okay with winging it and getting lost everywhere. Even stuff like navigating restaurant menus will be exciting brushes with the unknown (hopefully you don't have any food allergies).
-Your Rail Passes give you free unlimited bullet train rides, but you still need to obtain a physical ticket. This is done by talking to a person at the JR ticket area in bullet train stations. When you do this, you'll pick your train time and select your seats (if that option is available). I advise getting the ticket for your next train ride when you arrive in each city (since you're in the station anyway), as opposed to the next day, immediately before the next ride. Then you've got your tickets in hand and can plan around that instead of possibly wasting time waiting for the next train.
-As long as you're not traveling to the far north, you seriously don't need cold weather clothes. A sweatshirt, at worst, should suffice wherever, whenever.
-Not that I'm assuming anything, but if a foreigner is caught with illegal drugs in Japan, they get kicked out of the country immediately and forever. Not worth it. Plenty of cheap alcohol to keep you satisfied instead.
-Bring good walking shoes. Lots of walking, even in places with good public transportation.
-You can always rely on conbini for food/drinks/pharmaceutical needs, in a pinch. They're absolutely everywhere, with reasonable prices and quality stuff.
-Trains are not 24/7. They do not run all night. Be aware of this so you don't get stranded far from your hotel!
-Allow yourself some time to get to/from the airport. It's not in Tokyo itself (about an hour east by train when all's said and done).
-Get good map apps
-Japan is still a cash society. Don't count on being able to use credit/debit cards just anywhere.
-Exchange a bunch of cash at your local American bank (you have to place an "order" for yen ahead of time). Almost guaranteed to be a better exchange rate than the airport or wherever once you're over there.
-Consider purchasing a month of foreign roaming for your cell phone. Verizon charges around ~$80 but I found it very much worth it. Japan is not that great about wi-fi! Will come in handy when you're wandering and need a map.
-No matter what, there's going to be a lot of logistical figuring-out-of-things on the fly, so hopefully you/someone on your trip is good at handling crises under pressure (no one's going to stab you or anything; worst case, you miss the last train and have to spend the night on a bench in Shinjuku)

That's about it!