Because of the dietary restrictions among the OP’s group this might not work, but the advice we got from a friend who did a year-long ESL stint in Japan was to look for restaurants with a line made up of both tourists and locals. I don’t know the logic behind it, but the lines always moved quickly and the food was always excellent.
The challenge will be that I’m told restaurants in Japan do not make alterations, you order what’s on the menu. An otherwise vegetarian dish with bonito flakes or a pork soup base is going to come as is, they won’t change it for the customer.
My wife understands this and is prepared to accept what she can get even if she ends up eating a protein bar from a combini for lunch.
For those with food restrictions, I would suggest preparing a card written in Japanese that you can show the server.
I have used the JR pass several times when I have traveled in Japan and it has been very much worth it. If you do a round trip from Tokyo to Kyoto, it usually just about covers the cost of the pass. If you add several other trips along the way, then it even becomes a better deal. One year I spent time visiting a friend in Osaka for about a week. We used the rail pass to get to Osaka, and then to take several day trips to Kyoto, and one to Hiroshima with a stop at Iwajima. It was certainly worth the cost, especially considering you can use it on JR trains in Tokyo, which, although not as extensive as the metro, do get you to most of the city. While it is true that it is not worth it if you stay put, it can more than pay for itself if you are venturing away from Tokyo.
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Do you already use HappyCow? We’re vegan/vegetarian, and that’s how we find restaurants anytime we travel, whether it’s international or domestic. Japan actually has a lot of veggie places, but they’re often off the beaten path, sometimes underground or on some higher floor of a random apartment building, and they often speak no English at all.
The best ramen we ever had, anywhere in the world, meat or no meat, was a nondescript place in Kyoto called Uno Yukiko Gion Soy Milk Ramen… but it didn’t really have signage. It shares a building with a laundromat and AirBNB, but there was a line out the door. It was so unremarkable-looking that passers-by kept asking us “why is everyone waiting for the laundromat?”. It took us two hours to get seated, another hour to get our food, but it was totally worth the wait… probably in my top 3 lifetime meals. My mom, who eats everything and lives in Kyoto part-time, also agrees that it’s one of the best she’s ever had. We would never have found it without HappyCow… and that’s just one restaurant out of so, so many around the world. (Edit: On the other hand, the locals only give it 3.1/5 on Tablelog)
HappyCow can also help you find restaurants that aren’t exclusively veggie, but has veggie options. There’s also a gluten-free tag.
When you find specialist veggie restaurants (or at least restaurants that bother to make a special veggie dish), the food tends to be MUCH better than just ordering “_______ without meat” at regular restaurants. It takes more than subtraction to make a good veggie meal. The HappyCow top-rated restaurants tend to be “inspired by” local cuisines wherever they are, but made vegan/vegetarian on purpose and with proper nutrition (i.e., there’s an alternative protein and creative sauces and such).
Otherwise, many local street places will not have any vegetarian options at all, as even the rice (sorry, many of the sauces they put on rice) is often flavored with animal broth. On the other hand, there are many cheesy but meatless risotto and pasta dishes at the Japanese-Western fusion places. For the vegan, though, we ended up carrying a whole sack of 7-eleven rice balls (onigiri) as emergency food.
I haven’t used it but have heard of it. The bulk of our travel has been in Europe where we can generally find something my wife will eat - often pizza, pasta, or a sandwich. Oddly enough, we had amazing vegan ramen in Mexico City last winter. We ended up having dinner there twice in 10 days. I will add you recommendation to our list for Kyoto!
It’s easier in dairy-heavy cultures because cheese is delicious no matter what you put it on 
It’s harder in fish- and meat-forward Asian cultures, though. The app is free (or you can use the website), and really, really handy to have around.
You don’t have to find ALL your meals there, obviously, but every major city usually has a least 2-3 exceptional places that are worth checking out just for the food. It’s really its own culinary art (vegetarianized versions of traditional ethnic foods).
I didn’t try to make any alterations except at breakfast at my hotel, where i asked the waitress, “what’s that?” (Pointing at the of the little dishes) and she said, “eggplant”. I replied, "oh, I’m allergic to eggplant and took it off my plate, expecting the just skip that small part of breakfast. But she apologized, whisked it away, and returned with a little dish of giant sweet lima beans, instead.
Anyway, if you have the card they may be able to tell you what dishes you can eat, even if they can’t modify the menu.
Or, that happy cow app sounds good.
Huh… weird. Do they use a weighted average of some sort? It seemed odd to me that the ramen restaurant in my example has a 3.09 average score, but it doesn’t actually match the review distribution histogram OR inputting the 18 reviews into a spreadsheet (I got a mean of 3.72, not 3.09). How strange…
EDIT: Ah, yeah, they do use a weighted average. That explains it:
The ratings on Tabelog are not simply an average of the users’ respective ratings. The user’s level of influence is set to calculate the ratings. For Tabelog users who post regularly, the degree of influence is calculated based on various criteria, primarily to amplify the impact of those with extensive dining experience. Therefore, the level of influence varies from user to user.
It’s also interesting to actually read the text of the reviews. Many of them mention nothing but positives, but still end up giving it a 3 or 3.5. Is that just how the Japanese do it?
Yes. I’ve seen that in Amazon reviews, too. “This product did exactly what it claimed, and is well-constructed: 3”.
Honestly, i think that scale makes more sense. It lets you call out the unexpectedly good, as well as the unexpectedly bad. But it only works if all the reviewers are on the same page.
It should be noted that almost all onsen have separate baths for both genders and it is polite to hold a small towel over your pubic area as you move between the washing room and the bath. Don’t let it touch the water, though; deftly raise it as you submerge and either fold and place it atop your head or leave it at the edge.
If I could deftly raise my pubic area, fold it, and place it on my head do you think I would be spending my time reading the Straight Dope?
If you do want to go to an onsen, regardless of if you can fold your pubic area or not, it would be important that you remember the Kanji for Man (男) and Woman (女) because some Japanese Inns have a different design for each bath (e.g. one is partially outdoors), and will switch them at midnight so that guests can experience both. They don’t always have the signage in English to indicate which is which and if you go at an odd hour (like early in the morning) you might not be able to figure it out by who is entering which door. I have also been in restaurants and Karaoke establishments where there is no obvious signage (other than the Kanji) to indicate which restroom is which though that is rare these days.
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Here’s one area not mentioned. Nagoya. Home to Toyoda (yes, Toyota but the founder’s name). Started as an automated thread loom company. They still have one if not the first loom on display and it works. Museum quality displays take you through the history of fabric making and all the machines throughout history. Culmination is the latest computerized looms. They take your picture and the machine makes you an image, not with printing or dyes, but by mixing hundreds of different threads into the fabric. Enough on that. Toyota vehicles. A complete museum of all the cars/trucks etc… they made over time. Toyoda-san started with a mid-1920s Chevy. Ford’s antique Model Ts were already too antiquated. The Chevy was dismantled and engineers were tasked with improving every aspect of the car to make a Toyota. There are live engineering classrooms with students focusing on forging, stamping, combustion engineering going on inside the buildings. I could have spent the entire day there. That said, for the women, Nagoya is also home to Noritake China. A good restaurant, museum/display of all their patterns - and a factory store!
That looks like a long (but feasible) day trip from Kyoto.
It’s 34 minutes from Kyoto Station to Nagoya Station by Shinkansen (the express one, “Nozomi”); that’s really not bad.
Nagoya also hosts the SCMaglev and Railway Park, a museum showcasing the history of high-speed trains in Japan. Lots of rolling stock and other exhibits, and a daily lottery whose winner gets to pilot a bullet train simulator.
Another cool tech stop, this one accessible from Osaka: the Akashi Kaikyo bridge, one of the longest suspension bridges in the world. There’s a museum and a hardhat tour of the bridge that walks you out on the catwalk under the road deck, high above the ocean, after which you take an elevator to the top of one of the main towers. Quite a view from up there. When I was there eight years ago, many of the docents and tour guides were retired construction workers who helped build the bridge; they’re rightfully proud of their work and happy to show people around.
If you’re on a day trip for the bridge tour, Nunobiki Falls is also nice. There’s a ropeway just a short walk from Shin-Kobe Station that takes you to the top of the mountain. From there, it’s a pleasant walk downhill back to the station past an herb garden and of course the falls. Food is available at/near the summit ropeway station.
The site of the 1970 World Expo has been turned into a huge park, and it’s kind of a nice place to visit. the Tower of The Sun is still standing; a few years ago they allowed tourists with reservations to tour the interior, but I don’t know if that’s still happening.
Consider taking in a Hanshin Tigers baseball game at Koshien Stadium. The unity of the crowd as they cheer for the home team is entertaining. You can pre-order a bento that you can pick up when you arrive at the stadium, and women patrol the stands with kegs of beer on their backs, offering draft beer poured right there at your seat. To get properly kitted up before the game, visit Hanshin department store near Osaka Station; the “Tiger Clubhouse” there has all the fan merch you could ask for.
If you go to Hiroshima, try offsetting some of the the crushing sadness of the Atomic Bombing Museum with a visit to Miyajima. There’s an uncommonly large and ornate torii gate in the water near Itsukushima shrine; if the tide is out, people sometimes walk out to it. Also recommend the ropeway that takes you to the highest parts of the island, from which you can see miles in every direction.
If you like new architecture, Osaka Station and Kyoto Station are impressive buildings to behold. Kyoto Station was controversial because of its modern design, which doesn’t exactly mesh with the idea of Kyoto as being “traditional”. But there’s a lot to explore in both of those places, from rooftop to basement.
If you like old architecture - well dayum, there’s too much in Japan to point to.
Take some time to visit the basement of a department store. Most of them have a floor where they sell ornate confections - some prepackaged for gifting, and some made for taking home and eating right away - and most also have a floor filled with deli-style counters where you can purchase ready-to-eat foods to take home. Anything from salads to sushi to fried chicken, and a crazy variety in every category. These places get really busy around dinner time.
Check out a Hands store (formerly Tokyu Hands). Lots of home goods, but the big ones (e.g. 11th floor of Daimaru dept. store at Osaka Station) have a large arts and crafts section, as well as tools. Lots of stuff that’s different from what you might find close to home, interesting to browse and get new ideas and maybe pick up a unique tool or two.
You can purchase a sim or e-sim for Japan before leaving the US (assuming OP is from US).
https://www.amazon.com/s?k=japan+sim+card
Good to have that on hand before departure; you can swap it out during your flight so you hit the ground running when you arrive. When ordering, pay attention to data limits and time limits so you don’t come up short near the end of your visit.
Well ahead of departure, set up your Visit Japan Web account; a day or two ahead of departure, fill out all of the customs/immigration stuff so that you have QR codes ready when you arrive. This will save you some hassle at customs/immigration. Make sure each person in your group gets this done, or else make sure you do it on your account for everyone in your group.
Pro tip #1: Keep your password handy, because the VJW website will log you out after a short time and you’ll need to log in again before you get to the immigration desk. If your new sim/e-sim isn’t functional yet, get onto the airport’s free wifi while you wait in line.
Pro tip #2: The customs QR code reader at Haneda requires you to put your phone face-down on the reader. the VJW website doesn’t lock your phone display in portrait mode, so you will want to do this (lock rotation) before you get there. If you don’t, and you inadvertently twist your phone when turning it face down, your phone will go into landscape display mode and the QR code will disappear off the bottom of your screen before it can be read. I’ve seen people standing at the reader for several minutes trying to figure out why they can’t get their QR code read.
I used Google Fi, which worked everywhere i went in Japan, except for deep inside a quarry. Also, you can print that QR code before you leave. It comes out too big, but the customs employees know how to deal with that, and will take the piece of paper from you and hold it far enough away from the reader that it works. A large minority of passengers used paper QR codes when i was there.
Lots of good stuff to buy in Japan. There are excellent fans for sale all over the place (and also really cheap ones that are bulkier, but work fine.) i use my Japanese fans at square dances. They also sell nice sweat rags. Um, “Japanese towel” may be the English name. But it’s like a bandana, only long and narrow, and it is really more convenient than a bandana. I use those all the time, too. (Yes, i sweat.) I also picked up a cute pokemon-themed USB-C charger at the Anker store in a mall.
Oh, another tip: electrical outlets in Japan are us-style, but only have holes for two prongs, they don’t have the third hole for a grounded cable. That was the proximate cause for buying that charger; the laptop charger i brought has 3 prongs. Honestly, some of the outlets in my house aren’t grounded, and i use a 3-to-2 prong adapter for my electronics in those, and I suspect the same would be fine in Japan. And someone told me the hotel has adapters you could borrow. But be prepared with appropriate cords to charge your electronics.