Have you ever been to Jojoen?
Many consider it to be the pinnacle of "yakiniku" (usually known as Korean BBQ in the USA).
Everything about the food is as close to perfect as you can ask for from this type of restaurant.
It's expensive by yakiniku standards ($80-100/person) but IMO it's worth it.
Jojoen is one of the few semi-luxury dining experiences where I've felt the meal justifies the price and the hype.
If you want to take it a step further, try Rangetsu in Ginza:
http://www.ginza-rangetsu.com/(English page available)
There aren't many places where an "omakase" (
http://en.wikipedia.org/wiki/Omakase) experience will live up to the expectations, anticipation, or the bill, but IMO this does not disappoint.
The key is to go for dinner, not lunch during which you are served yesterdays's leftovers.
At Rangetsu was the first time I experienced grilled kuro wagyu (A5 black beef- rated best in the world) topped with fresh sea urchin (uni).
One of the most amazing food experiences in the world.
For Kyoto, one of the best dining experiences there is a place called Nomura Sansou (
http://www.nomura-sansou.com/).
The use a brand of chicken called Nagoya Cohin, widely considered to be the best chicken Japan.
Unbelievable meal.
It's reservations only and you can only get there by car/taxi but definitely a unique experience.
I remember the price being around $300/person for a overnight stay but for dinner only it's probably around $150/person.