What to do and not to do in Japan:
Firstly, you have to make sure that all your travels are well thought in advance. If you arrive in Tokyo, chances are that you will not want leave the city, unless you already have booked trips (tip#1 book a week train pass prior to arriving in Japan - once there, the deal is off. It will cost about $300/person and it is a "free" pass for wherever you go, speed trains and city trains, minus subway, included. Great savings, given that just one way Tokyo-Kyoto is $160/person. Yep, transportation is expensive as hell)
Tip#2 Don't NEVER be late for breakfast (at inns and personal homes.) I swear to you, it is seen rude turisty behavior , even if you have a good reason. And this is because local people want to give you the best experience, and perfectly cooked and served food is a personal pride. If you are late, the salmon will be slightly cold, the rice 30 seconds overcooked, and this is perceived as a disaster.
Go to the mountains. Take at least 2 days. Hot spring baths and great breakfasts. Try the Thai massage (amazing, though there is a LOT of touching. Inoffensive, nonetheless) Must wear a yukata - that is, you have to learn how to put it together. My take, listen to the one-on-one instructions, otherwise you'll be lost. For guys is easier, they just have to put on a traditional simple robe.
Visit the temples and shrines. Try early morning. Tip#3: Early early morning. You'll have the whole place to yourself and the feeling is indescribable. All shrines are surrounded by meticulously thought zen gardens. Every leaf is occupying its designated space. Look at the photo on the right. That is architecture.
There are 3,500 temples in Kyoto only, going from , size wise, back garden to over the hill. But there are a few that you must see:
Sanju-San Gen Do (temple - where the 1000 Kannon statues are. Well, 980 only, for 20 are reconditioned each year - how long it takes to do all?)
Gold Pavilion (Kinkaku-ji) Temple - the most amazing thing I have seen. Ever.
Silver pavilion (Ginkaku-ji) Temple - the most amazing thing I have seen. Ever.
Ryo-an-ji Temple (zen rock garden) - this is getting old... the most amazing thing I have seen. Ever.
Kiyomizu Dera (temple, of platform on stilts).
Fushimi Inari Shrine (fox shrine of 1000 gates...and 1 million steps- try the soy ice-cream if you make it to the 3/4)
Back in Tokyo:
If you are a late sleeper, you won't be able to get one of the 120 tickets/day for visiting the fish market. Legally. So, enjoy the extra hour of coziness and warmth, and be there by 5am! If you are lucky, you'll manage to (tip#4) sneak in clandestinely, walk towards the end, and seethe tuna auction pit. I resisted for the length of 10 photos after which I was spotted and escorted outside by a security guy with no sense of humor (and I tried my best) with a man silhouette crossed by a red X sign on his uniform. Trust me, it is an experience you don't want to miss. The auction starts at 5:20am.
After the chase through the market, 5:30 you are looking at a 3 hours wait for the best sushi in the entire world (Photo left and right). I mean it. All of us who ate there mean it. If you are human, you will love it too. 3 hours (no exaggeration, if you are there at 10am, you'll eat at 1pm), 2 coffees, soldiering against the razor sharp fish breeze from the market across the street, careful not to be run over by the strange carts with front motor that only care about their fish deliveries, all for 11 (E-L-E-V-E-N) pieces of sushi. Made by God, for I am now sure that God is a sushi master chef.
Shopping: Japan is anything, from high-end to cheap-chique, from classic to urban. You need to make sure that: (1) your CC company knows that you are there - otherwise, know that it will block your card - living proof on the left, waiting in line with the US; (2) bring an extra travel bag - you'll need it; (3) they will walk you to the exit of the store where they will handle you the shopping bag. it is a politesse you'll eventually have to get used to.
Do eat at hole-in-the-wall food joints. Tip#5: Remember, there is no tipping in Japan. These places usually have a machine at the entrance; choose your menu, get a ticket and deliver it to the food-barthender. Sometimes, they are only bars and you eat while standing. About street fairs: all you can eat. Literally, grab as much as you can (for $$) not because it is cheap, but because it is all good. (Except for the fruits in soft candy or whatever they are called. So sweet it hurst. Your dentist, and I, would be strongly against it.
Don't smoke in the street - (tip#6) Buy a portable ashtray and don't walk while smoking, or you'll get fined. If you cannot wait for the special amenities (rare in Japan) and don't have the key chain ashtray, there are plenty coffee shops and bars which can accommodate you.
Drink plum wine.
Tip#7: all train and a lot of the major subway stations have lockers, an inexpensive way to leave your stuff if you're in for a stroll.
Lastly, you haven't really been to Japan if you did not see a Sumo tournament (here @ Osaka, 14 games, one afternoon of pure excitement. Pay the price, it will pay off. Go towards the end, last couple of days, so you'll see the best wrestlers. I have seen the last year winner, who now had a clear 11-0 record, and he just won the 12 match.)
You must visit a Japanese cartoon porn store. Enough said.
You cannot leave the country before singing in a karaoke bar. Bellow, with the best voice of the evening, sorry all others, and a beautiful presence)
Little useful inventions: banana vendor machines, restroom map for when waiting in line, green tea latte (try anything made with green tea.)