Echoing Latia's rec, as the Japan Travel Planning group on Facebook is incredibly helpful. I read through dozens of threads to see itineraries, get ideas, and be inspired (there are some incredible amateur photographers out there!). For what it's worth, we spent 9 days in Tokyo (and did not go to any other parts of Japan) as we have a more leisurely travel style. We landed at 7 pm Tokyo time and then did 1-2 activities per day. I booked almost our meals in advance since many of the more popular/upscale ones require reservations. Some restaurants do NOT accept reservations so I noted that below, too.
Day 1: Arrived at NRT at 7 pm. I had booked a private transport so we wouldn't have to figure out the train system. The driver was not waiting for us and after 2 phone calls and 20+ minutes of waiting, I canceled it and just paid for a taxi (which is ridiculously expensive and should probably be avoided--$330 US to go to Shinjuku).
Day 2: Most restaurants don't open until 11 am. We bought a ton of food from the konbini (aka convenience stores like 7-11 and Lawson's). We loved their egg salad sandwiches (creamy egg salad on soft crust-less white bread), fried chicken cutlets from Lawson's (DH got a batch hot out of the fryer and they are far better than any American fast food chain like Popeye's, KFC, etc), sushi bento boxes (we got hand rolls, inari, and nigiri that rival our typical suburban American sushi restaurants!), etc. After 11 am, we took the metro to go to Takashimaya Department Store to check out their basement food hall. Tons of great options and we ended up eating lunch consisting of nigiri sushi, tonkatsu bento box, and desserts. Dinner for my birthday was at Yoriniku, a nicer yakiniku (Japanese BBQ meats) restaurant. We made a reservation through JPNEZY (a website that charges about $8 US for a reservation for 4 guests).
Day 3: Same breakfast from konbini. Had an 11 am street food tour on Sunamachi shopping street with Kanako from an AirBnB experience. We're very food-motivated so this was a fun way to explore an older part of Tokyo (felt like all locals were there as we didn't see any obvious Westerners/tourists) and eat some great food (incredibly delicious udon, 3 choices from a Japanese "deli" which were fried tofu stuffed with pork, bamboo shoots and vegetables, and soy sauce potatoes, scallop and sea bream sashimi (plus the chef sent the girls free amoebi sweet shrimp), taiyaki (fresh fish-shaped waffles stuffed with red bean, custard, or sweet potato--surprisingly, sweet potato was the best!), unagi skewers, a spicy fish paste, bean sprouts, leek, and carrot pancake (which Kanako said is one of her favorites), and tempura pickled ginger slices (another one of Kanako's favorites). Dinner was at a small ramen shop around the corner from apartment,
Menyayuusaku.
Day 4: We did a morning family photo shoot in Shibuya Crossing with a Flytographer photographer and then went to enjoy the Japanese mineral baths (aka onsen), SAYA-NO-YUDOKORO. They offered a stunning kaiseki lunch (multiple courses including shabu shabu, sushi, artfully arranged vegetables, homemade soba noodles, etc.). Dinner was Udon Shin in Shinjuku (awesome handmade udon, no reservations so we went at 4:30 pm to avoid the 1-2 hour wait and only had a 15 minute wait!).
Day 5: DH and I did an upscale sushi lunch at Sukibayashi Jiro Roppongi Hills (had to make the reservation on Voyagin, which charges $70/person just for the reservation). Girls stayed in the AirBnB and ate konbini food. Then I took the girls to do a Kimono rental with Kahori in Harajuku by Take****a Dori. See her Facebook page
https://www.facebook.com/sakaeya2daime/. It's a small shop only open by appointments and Kahori's family has been in the kimono business for decades. It's not the typical tourist option as you can tell kimonos are a passion for her. She also did a lovely tea ceremony for us. Afterward, we ate a bunch of street food (including the GIANT rainbow colored cotton candy that Instagrammers love on Take****a Dori, plus crepes, soft cream, and candy). Dinner was split up since my youngest DD has a fish allergy. I took our eldest to eat at a kaiten zushi place (conveyer belt), Himawari Sushi Shintoshin, while DH took DD2 to eat at Coco Curry to get a curry chicken rice bowl.
Day 6: DH and I did another high-end sushi lunch at Sushi Masuda (again, $70/person to book the reservation on Voyagin). This was the best meal of our life and truly incredible. It's a tiny 6 seat sushi counter and just stunning sushi quality and precision. The girls walked themselves to the Coco Curry House since DD2 wanted to eat it again and DD1 hadn't tried it. After lunch, we got the girls and went shopping at Oriental Bazaar in Harujuku. We bought a ton of souvenirs (scarves for grandmas, sakura tree seeds, Godzilla boxer briefs, coin purses for friends, Tokyo t-shirt, chopsticks, bowls, and a set of wind chimes). They have really nice quality products for reasonable prices. Dinner was at Shinjuku Tsunahachi Tempura, made via JPNEZY for $8 US flat rate for 4 people. We aren't big tempura fans, but everyone raves about this place. It was good but not mind-blowing and DH felt it was still a bit too much fried food.
Day 7: By this point we were sick of konbini food for breakfast but you can't bring home restaurant leftovers and very few places sell take-out. I found a kebab stand near the Okubo station, Saray Kabob. They always had a long line between 11 am and 9 pm when we walked by and it smelled amazing. Tasted just as good as it smelled! We actually went back a second time to get more! Anyhow, we went to do the TeamLabs Borderless digital art experience this day and it was AWESOME. We went at 9:30 am (they officially open at 10 am) and it was great to do the popular Lanterns room (where they only allow 8-10 people in for like 2 minutes) twice in a row before there was a line! I strongly recommend it, not just for those who love Instagram! Since we were way out in Odaiba, we ended up having lunch at the Sakura Restaurant at the Hilton. Overpriced and fancy hotel food (entrees were between $50-85/person, as 10 year old DD2's lunch was the $85 Kobe beef summer pot), but the sashimi, sushi, and "simmer pot" were far better than Wendy's or other tourist food. We then went shopping on Kappabashi St (known for kitchenware, knives, ceramics, etc.). While DH shopped kitchen goods, I took the girls to walk to Asakusa, Sensoji Temple, and the giant Don Quixote store (sort of a like a Target but I didn't see any clothes) to buy $50 worth of flavored Kit Kats (green tea, ube, sweet potato, dark chocolate, wasabi, peach, and ruby chocolate). Dinner was at Sushi Bar Yasuda, a sushi bar that caters to foreigners (made reservations directly on the website and chef was in the US for many decades and speaks fluent English).
Day 8: Ate leftover kebab for breakfast again. Went to Katsukura in the Takashimaya Department store for an awesome tonkatsu lunch. We stopped by Joel Robuchon’s bakery first and picked up 2 chocolate croissant, 4 curry pan, 1 mushroom/cheese croque monsier, and 1 regular croissant. Spent a couple hours shopping at Tokyu Hands and also went to the Flippers Stand inside Shinjuku Station to get the souffle pancake/pudding treat. DH and DD1 shopped a couple hours at Uniqlo. Dinner at Torishige, a yakitori restaurant and I made reservations on JPNEZY. Their menu had limited English and the wait staff said their Mandarin Chinese was much better (but I only have a basic understanding) so I don't quite know what animal parts we were eating (pig cheek? cow intestines?). They did substitute items like a simple steak skewer for a few of the "weird items" for the kids.
Day 9: Ate all the leftovers in the AirBnB, did one last outing for more curry pan (but Joel Robuchon didn't open until 11 so we found a place in the Shinjuku station after 45 minutes of wandering that crazy station!), and then ate sushi at the ANA airport lounge for our last meal in Japan. I booked a flat rate taxi company to take us back to NRT, so it was about $250. You can take the train but it's not easy with so much luggage. We did carry-on only to Japan but had to use duffle bags to bring back stuff we bought.
Let me know if you have questions. Our trip was all about the food with some shopping and light activities. We loved Tokyo!