First off, thank you to all of the folks who take the time to post their trip reports here, and all of the kind folks who take the time to answer questions. We did some really good eating in Japan using your advice. Hopefully this writeup will be useful to others planning future trips!
We started the trip in Hakone, staying at Yamanochaya ryokan. It's a beautiful place for bathing and relaxing, and some of the food was good, but some of it was definitely not good. For instance, I just loved the Japanese breakfasts, with grilled fish and yummy eggs and rice. But the kaiseki dinners were not cooked start to finish by someone with a lot of skill. I have never not loved any preparation of foie gras, but theirs was just gross (overcooked, basically steamed to death, a tragedy). Bottom line: I wouldn't come here for the food.
We stayed in a machiya here, run by a little company that was willing to make restaurant reservations for us, which was fantastic. Our machiya was adorable, and we were very happy to have the extra space that a townhouse provides, vs having to stay in a pricy hotel just to use their concierge service. I highly recommend going this route.
Nakamura (the tiny chicken place in Gion, not the expensive place)
This was a Chowhounder recommendation and it was so good! Chicken sashimi, chicken shoulder, chicken liver (and some vegetables as well) - all were perfectly executed and delicious. Plus the chef was very nice, and it was a good value. Nice options for wines too - had a chenin I really enjoyed. Definitely go here!
I think I will remember Kyoto as the place with way too many tourists and the best chicken on earth. This place also hit it out of the park - possibly our favorite meal of the trip. We had nearly the whole menu, the innards being particularly outstanding, but really everything was great. The family (?) that runs the place were super sweet and friendly, and really made it a nice experience. They also had some nice wine, with some natural options. One of the first French 2015s I've actually enjoyed. I would eat here on a weekly basis if I could.
This little yakiniku place was also great. The chef was very kind and worked with our really non-existant Japanese very well, and even the other patrons were helpful, telling us what to eat with what. The quality of meat was excellent, though I couldn't tell you where it was from. Among many grilled things were some delicious fatty tongue, super marbled muscle cuts and fatty intestine (or stomach?), plus a selection of goodies to eat raw, like heart, tripe and maybe shoulder. If you go, prepare for it to be smoky.
We had a nice lunch here, although it is overshadowed in my memory by the three great restaurants above. Their sashimi of a super fatty yellowtail (never had anything in the US like this), stewed octopus, crab salad, and rice in a banana leaf were particularly good, the rice being some of the best we had on the trip (and it looked like a tamale, which was fun). Again, the chef was very nice.
We ended up at this affordable lunch kaiseki place after encountering insane lines elsewhere on the one day when I didn't book in advance (word to the wise - definitely reserve in advance!). It was a little tricky to find, but was an oasis of calm once we were in there. Having had "kaiseki style" meals at our ryokan that were kinda meh, the difference in technique and quality were obvious here. I won't go into everything we had but I will forever crave their soy sauce foam, served with the sashimi course instead of regular soy sauce. Usually the inclusion of foams have me rolling my eyes, but this served the purpose of both lightening the saltiness of the soy and helping it stay where you put it on the fish, as well as adding new and interesting dimension with texture. Takuma was also a very good value, as the set menus were about ¥4000 pp.
We showed up here maybe 50min before opening time, and there were already about 5 people waiting inside. This turned out to be the right move though, since we got to wait inside, seated, the whole time drinking tea and perusing the menu. Then our food was ready almost exactly at opening time when we were ushered in to sit. When we left, the line was truly insane - I cannot imagine how long those folks had to wait; certainly over an hour (this was a Saturday, in one of Kyoto's busiest tourist seasons). Food was all good and a very good value (I had the spicy udon with burdock tempura that is their specialty), but not earth shattering. My partner loved his curry, but I found it way too sweet, so be forewarned.
This tofu-focused restaurant is a beautiful place to have lunch, relax and get away from the crowds - our view out of the window was enchanting. However, while I was hoping to come here and be convinced of the awesomeness of tofu, it was mostly just ok. The best by far was the tofu skin. The rest of the food was fine, but not memorable, and I enjoyed other tofu preparations more elsewhere. The wine here was vile - do not get wine.
I wanted to have some fermented sushi while I was here, so we went to this weird little place. I thought at first that they were just seating us in the waiting room to wait, but that's actually where you eat. It was very strange and very small, and kinda like an upscale doctor's office. The fish itself was delicious, especially the mackerel, but the cost performance was very very low. We spent ¥5300 on tiny food (6 pieces of sushi each) and no drinks, and my partner needed another dinner right after. I'm very glad to have tried it, it was a lot less weird than I anticipated (like regular sushi but more firm, a bit larger, more vinegared, nothing funky about it, good for a fatty fish lover), and I'd love to eat it again, but it's a bit overpriced.
We went for okonomiyaki after Izuu. The okonomiyaki itself was fine - drunk kid food. The rice cakes involved were particularly good. But if you go here what you really must get is the pork wrapped in egg. It was like a perfectly cooked omelette filled with barely set, super juicy, bacony cooked pork. I don't know that I'd do this again though unless I was drunk and had the munchies.
Against the advice of some Chowhounders, we wanted unagi, so we went here. Yeah, it was crazy overpriced in relation to some of our much better meals like Nakamura and Hitomi, but it was also delicious and we (2) polished off the bamboo steamer set for 3 in no time flat. I loved how mild the eel was, and how not sweet and complementary the savory sauce was (here in the US, eel is almost always super sweet). I would not spend the ¥10000 again, though I am definitely glad we tried it once.
We stayed at another ryokan outside of town called Wanosato. Unlike Yamanochaya, and totally unexpectedly, the food here was outstanding, and our first kaiseki meal here was one of our favorites of the entire trip. The technique was there, but there was also a creativity and personalization to the menu that made it special. For instance, they served us fish from the river that runs along the side of the ryokan, grilled over the traditional fireplace in the center of the old mountain style building. The quality of ingredients was there too - both mornings they treated us to the most unctuous, melt in your mouth Hida beef grilled on a hoba leaf in miso, and our second dinner was this unbelievably marbled Hida beef shabu shabu. They also served soy milk in the morning that cooked itself into tender, soft tofu in a little pot right in front of us with the most delicious sesame sauce (being completely ignorant of tofu, I had no idea this was how it was made and it kind blew me away). Apart from the food, the hotel was very atmospheric, with the constant fireplace smell and the sound of running rapids outside. I highly recommend a stay here.
This is a touristy place in town that also does the Hida beef on hoba leaves. I went at the urging of a friend who just loved it, but I think we either hit them at a bad time or ordered wrong because it was unimpressive. I was really glad that we got a surprise do-over on the Hida-beef-hoba thing the next morning at our ryokan though because THAT was indeed very delicious. Bottom line, I'd skip Suzuya.
Harada Sake Brewery
You can taste about 20 sakes from a fridge (self pour) for the cost of one little sake cup that you can then take with you (¥200). It's a great deal and a few of the sakes were quite nice (I really liked the cloudy one that tasted like cheesy yogurt), but the BEST thing here, and you can find it also at the brewery across the street, was the packaged Hida beef bacon jerky. The fat had that melt in your mouth quality of the Hida beef... paired with everything you love about bacon and jerky, this was a big winner, and we had to go back to buy more of this TWICE. Was it beef or pork? Not sure, don't care.
Hirase Sake Brewery
We paid to taste three sakes here, and the quality was a clear step up from Harada - we even bought some. The place was empty, but it also gave less of an impression of a tourist gift shop like Harada, and more of a working warehouse where they make and ship sake. Ultimately I'd recommend a visit to them both.
We stayed at the Cerulean Tower and they very kindly made all of our reservations. It was a nice place to say, but not as charming or roomy as any of our previous accommodations.
Sushi Takumi Shingo
After pouring over all of the sushi advice here, we chose this one for our big blowout evening meal, and Shingo san did not disappoint. The fish was all delicious, just creative enough, and the atmosphere he created with his sous chef and banter with the clientele was boisterous and fun. We also noted that the patrons were generally young and hip (all Japanese), which was a little of a surprise to me. Anyway, I wholeheartedly recommend it!
We had a very nice lunch here, and again the chef was just lovely. The meal was great and a good value. I will say that I don't think this was particularly better than high end sushi meals we have had in NYC though (which others here had noted previously). I would say certainly 15 East (with Masa) and even Shuko were better than Iwa, but Takumi Shingo and 15 East are closer to on par. I do prefer the more creative chefs - for instance Ichimura at Brushstroke to me was very good but forgettable - Iwa was similar.
All the meat and innards here were outstanding, but comfortable it was not. It's super cramped and SUPER smoky in here (I cried and cried from the smoke, and smelled for days), so don't go unprepared, and do try to sit in the outer room. Still, I would absolutely return for the tongue, glands, and other yumminess.
We got here early to avoid a crazy line, but since it was a weekday, we needn't have. Service was kinda slow and it was very cold inside the restaurant, but the quality of the soba noodles did shine. My partner was bold and got the natto and egg version - this was much more delicious than my soup and I would absolutely get it again. Ever since watching Hard Gay torture kids with natto a decade ago (https://www.youtube.com/watch?v=5poga...), we knew this was a must have. It did smell like funky cheese, and the stringyness is a little icky, but it's fine to eat. It was stellar with runny raw egg and these noodles. The grilled shrimp and tamago were also very good here.
We really enjoyed our tempura omakase here at the counter. Some of the highlights were another super tender eel (anago this time), fried scallops, cuttlefish, uni in shiso, oyster with cheese, and of course shrimp heads and bodies. It's a bit packed in there at the counter, but that's where you'll want to sit, and to do so you should reserve in advance.
We waited in a fairly long line here, but it moved fast, and the ramen was indeed delicious. I am not a big fan of ramen (prefer udon and soba), but I love yuzu, so the spicy yuzu with the substitution of the thicker shinku temomi noodles was perfect for me. I was really impressed with the pork here - they got a great char grilled flavor on it over the charcoal. Next time, I'd order extra pork for sure! This place was great.
We got here about 45min before opening per some advice on Tabelog and that was just right - the line got REALLY long REALLY fast after that. We were in the first seating, but unlike at Yamamoto Menzo, things here did not move fast, so if you were not in the first seating, you'd be outside for quite a long time. The tonkatsu pork chop was giant, juicy and delicious, covered with a super crunchy crust of panko and resting on a bed of delicious shredded cabbage - really nice stuff. The full meal here was a very large portion, so come hungry. They even put pork in the miso.
We ended up at Uoshin as a third choice for izakaya after getting negged on reservations at both Kotaro and Nakamura. We weren't super impressed with it, but we did have some interesting things like grilled milt, tempura smelts rolled in shiso and herring roe. It was a little smoky in here as well. It's a good backup, but I certainly would not go out of my way to eat here.
Lotteria Burger & MOS Burger
My partner wanted to try some fast food burgers, so we did. For me, Lotteria won by a mile, but again, it's just a fast food burger, nothing special or particularly great.
Suzuki Fisheries in Tsukiji Mkt
We were lucky that Tsukiji did not move on time, so we got to visit before it closes. I had a very generous uni don here at Suzuki, and my partner had a chirashi that looked very nice.
Kujira no Tomisui in Tsukiji Mkt
Where else are you going to try whale other than Japan? So we did. The whale sashimi was good - very lean, meaty, iron rich, like a cross between lean beef and lean tuna. Not amazing but fun to try. The whale bacon was fishy and fatty in the extreme, well beyond mackerel, very strongly flavored, and eaten with salt. I thought it was pretty good but the taste really does stay with you. The fried whale cutlet was fine -- forgettable -- one of those fried things that just tasted of frying. I can't say I'll miss eating whale, but my stomach is prepared for a career as Captain Ahab's assistant should the opportunity arise.
I love natural wine, and so does Japan, so I needed to hit at least one natural wine bar (we also went to Deux Cochons in Kyoto but just for wine). This was a great choice - the food was more french - beef rillets, sardine confit, homemade breads fresh from the oven - but very well executed and perfect for the wines. I was interested to see that they rotate their by the glass offerings as the night goes on - they just pop a bottle or two of one and then move onto something else - so we got to try really quite a lot of things by the glass, some that I knew and others that I did not. I had been on a mission to find some Japanese natural wine, and while they didn't have any here, I was able to find some at a shop in Ginza. Anyway, Ahiru store is lovely and the folks there are super nice.
If you like Scotch, there may not be a better place for you on earth. It is super tiny, and super smoky, but this guy has been collecting rare whiskies for who knows how long and has amassed a truly impressive collection. We drank some whisky older than me! He's got Japanese whiskies too, but it's the Scotch collection - many from long-closed distilleries - that is the real draw. Prices were surprisingly modest and certainly very fair. A must do for the whisky lover.
If you read all the way to here, bravo. Hope this is helpful for someone in the future and happy travels!