Thanks again for all of your suggestions. We had a truly excellent time in Japan and I'm already planning my trip back to Asia! Here's a quick roundup of all the spots we tried:
Birdland: we did the yakitori pre-set menu. The chicken was moist, tender and so flavorful. The gingko nuts were definitely something we had never tried before either!
Tsukiji Market: I'm not sure of the name of the place (photo attached if anyone can translate), it was a couple of doors down from Sushi Dai and packed with workers from the market, so we thought it was a good bet. Sushi was delicious, of course, and the miso soup had fish in it, which was something new for us.
We tried out many, many pastries at Mitsukoshi and Matsuya. I think my favorite were the sandwich cookies from Circa.
Sometaro in Asakusa: this is where we went to try okonomiyaki. I hope I can find a decent version in NYC because we absolutely loved this. The waitress helped us cook everything and it was great to be able to take off our shoes and relax after sightseeing.
RyuGin: beautiful, as expected. I've never seen more elaborate and gorgeous plating. Standouts were the crudos and the sake ice cream and souffle at the end.
Rokurinsha on Ramen Street: I had no idea that ramen could be taken to this level. The broth was so rich, so complex and so incredibly tasty that I don't think I'll ever have a better one. Definitely worth waiting in line for (again and again).
Maisen in Harajuku: again, so much better than katsu stateside. We ordered what everyone else seemed to be getting (pork cutlet with the shredded salad) and it was crisp without being too heavy. The dipping sauces were my favorite part, I especially loved the one with apple.
Sushi Mizutani: This was probably one of the most special dining experiences I'll ever have and it wasn't necessarily because of the food (which was fresh and fabulous, of course). We were lucky enough to get seated next to a woman who was fluent in English and Japanese (as well as being a regular) and by the end of the meal we were doing shots of whiskey with Mizutani himself. What a charming and talented man! Even if you don't speak a lick of Japanese, like us, totally worth it.
Airport sushi: we stopped at Kyotatsu twice during layovers and it was a super enjoyable meal served very quickly. I recommend the tuna special.
Treats: I couldn't believe the variety of KitKats! We stocked up on both regular matcha and sakura blossom matcha as well as strawberry cheesecake and spicy chocolate. I was too skeptical about the wasabi to try, haha. Also loved trying all the Tokyo Banana products, but I think my favorite were the caramel banana sponge cakes.