This is already an epic thread. I unfortunately will not be able to visit Japan again any time soon, but will live vicariously through all of you. Will still throw in my $0.02.
I agree with most, especially if it’s your first time in Japan, to definitely visit Kyoto and Tokyo. Kyoto for the history (even if sometimes a bit touristy), and Tokyo for the sheer scale. Sure it’s a metropolis, but it’s still a distinctly Japanese metropolis.
A couple other things before getting to food - I personally just get the international pass capability if your operator offers it (I know Verizon does but don’t know who you have). It’s $10 / day, which is not much different than a personal Wifi, and you can use your data quota overseas.
Also, as you are probably doing both Kyoto and Tokyo, I assume you’ll take the shinkansen aka bullet train. That’s an experience in and of itself in Japan (so serene, so efficient), so I it’s an experience to try.
And of course, on the shinkansen, don’t miss out on “ekibens” or train station bento boxes. Yes they’re highly processed, but I think they’re a delicious.
A couple ekibens and a saba bozushi from a train station.
In terms of timing, for a Feb visit, you might be a bit too late for some of the higher end restaurants, especially in Kyoto. For a number of restaurants though, reservations open up on Jan 1 for February so would contact your hotel before that.
Also, I personally had a good experience with Tableall - sad to see @J_L ‘s experience was not the same, and his data point is more recent than mine. I would say they have exclusive access to a few restaurants - e.g., Sushi Kimura in Tokyo only allows foreigner reservations through Tableall. I was able to book at Kimura a few years back this way.
Kyoto Recs
Agree with what @Bagel said. Some background though - I don’t know enough to be authoritative about this, but kaiseki in Kyoto is more traditional than what you’ll see in Tokyo, and as a result, the flavors can seem austere to a lot of folks. So I can see why many don’t feel Kyoto kaiseki meals are “life-changing” whereas the ones in Tokyo might seem more special. That said, I have a couple of recs for Kyoto
My FTC post about a recent Kyoto (and Tokyo) trip is below
Sumibi Kappo Ifuki
My avatar shows a dish from here - this restaurant focuses on grilled foods, so it’s a pretty unique place even for Kaiseki. FYI, Ifuki is a 2 star Michelin - I’ll list this info for informational purposes below but it shouldn’t necessarily be a deciding factor for you.
Hyotei
Hyotei serves kaiseki and is as old school as they come - it was founded around 400 years ago and was a destination for pilgrams to Nanzenji temple. It’s a 3-star Michelin restaurant - I am actually recommending the lunch “shokado bento” for 6000 JPY at they Hyotei Annex, or their breakfast and not their dinner. It’s an “accessible” way to try 3-star Michelin cuisine but with a much lower financial and time commitment.
Ryuhei Soba
A reasonably priced soba set menu - we tried this during lunch. It is a bit of a schlep away from the middle of Tokyo. I highly recommend this for the quality of soba and the great other types of food you can try.
Jiki Miyazawa
This is a one-starred Michelin restaurant that focuses on Kappo (counter) cuisine. The original chef, Masato Miyazawa originally opened this place but has since opened Godan Miyazawa and cooks there now. Jiki Miyazawa still has a lunch course around 7000 JPY that gives you a nice sampling of kappo cuisine.
The below is some tofu is ground sesame
@tktktktk you asked about tempura and one place I really liked in Kyoto was Kyoboshi. However, there are numerous, numerous places in Tokyo, so you might want to try those.
I would also highly, highly recommend MItsuyasu (**), a kaiseki restaurant - some of the best vegetables I’ve ever had. But I think the restaurant books months (i.e…, > 6) so not sure if it’s feasible now.
Tokyo
For Kaiseki, in addition to what others recommended, I would add two, though both are very pricey (with premium quality ingredients to match).
Goryukubo **
This is, of course is one of the places where Chef Brandon Go trained (the other being Ishikawa) before returning stateside. It’s ** dining, and I think reservations are a lot more straightforward to get than some of the other kaiseki restaurants. I’ve had the good fortune of going twice and both meals were fantastic.
My post is here:
Kimoto
This is the restaurants where I had my favorite kaiseki meal, which means it’s probably my favorite meal ever. Resys are pretty hard to get (log on Omakase right on the dot) but if you can swing it and get it, it was pretty life changing for me.
Post here:
For sushi, my favorite sushi meals ever have been at restaurants that serve Jiro-style sushi. I’ve never been to the honten location of Sukiyabashi Jiro, but I’ve had the pleasure of dining at Mizutani (now closed), Harutaka**, and Sushi Masuda**. Chef Harutaka Takahashi and Masuda Rei were both apprentices of Jiro (Harutaka left before the documentary, but you can see Masuda-san in the documentary). I view Jiro-style sushiyas as places where you’re not going to get a lot of types of fish you haven’t tried elsewhere, but what you will get is pristine quality neta served on sharply acidic komezu (white vinegar) seasoned rice.
Harutaka ** is open late with 2 seatings, so reservations are pretty feasible. Due to the hours, and of course the quality, it’s evidently a favorite of other chefs. I will say relatively speaking that the nigiri, and not otsumami, is the strength here.
My post here:
Sushi Masuda **
I believe he closed his original Tokyo shop in Omotesando and moved to Taiwan for a period, but is not back in Tokyo and opened a new version of the shop.
Sushi Kimura
A break from the Jiro-style places above - Kimura-san serves super aged fish, and I think the execution is really good. It’s nigh-impossible to reserve, but Kimura-san speaks good English and I think still takes reservations through Tableall.
Non sushi/kaiseki meals 
Ramen
Tsukemen (like what they serve at Tsujita) can be transcendental here. As others have mentioned, you’ll line up at good ramen places. I really really liked Rokurinsha and Menya Kissou. Gonokami Seisakujo is really good, though it’s a very very specific type of tsukemen (the dipping broth tasted like seafood bisque to me).
The tsukemen at Rokurinsha
The line at Rokurinsha
The tsukemen at Menya Kissou
The line at Menya Kissou (with seats to relax once you get into the first 10 spots)
The ramen at Gonokami
(you guessed it) the line at Gonokami
Ramen Mugi to Olive was a shop in Ginza that was really good and didn’t have a line, so might be a good last minute drop in.
Udon Maruka
I like Udon Maruka - the noodles are perfect, and they have all sorts of preparations. I recommend getting a cold udon to better appreciate the texture.
Toriki *
This is an old school yakitori place - the chef speaks pretty good English. Just to be safe, I would personally not eat the livers / organs rare again.
Moyan Curry
Mini chain in Tokyo and has the best Japanese curry I’ve every had.
Depending on how much you want to splurge, I think wagyu in Japan is different from eating it here and worth trying. The price extends into the stratosphere, but a pretty good place to try is a micro chain of teppanyaki restaurants called Ukai-Tei. There’s one in Ginza and I believe one in Omotesando. Think Benihana on steroids but with high quality cooking and premium beef.
If you want to really go all out, you could go to Shima or Dons De la Nature - I had good meals at both, but (especially at the latter), I left with a much lighter wallet.
Can’t recall if others mentioned this, but of course also visit the deepachikas, or food courts in the departments stores!
