I spent two weeks in Japan last May. And probably spent other 10 months planning and reading (this forum of course) before the trip. This is some advance from my experience.
Note: I know every person is a different kind of traveler. So, take that in consideration. This is only a point of view.
PLANNING THE ITINERARY:
I spent so much time reading all forum and blog posts before traveling that I knew maybe too much of what I was going to experience. Actually the weekends after spending hours reading so much information I used to end stressed.
When I read a request for Itinerary and see a day by day detail of the places and things to be done, I remember that time and simply close it.
My recommendation: Do a proper research on what to see and where you want to do, but don't over plan. Puting so much things on a same day won't let you enjoy the trip enough. You better have MUST DO's and map other places you want to have on your radar. Once you are there, you meet people, places, manage weather, etc, you can make your own decisions.
FUNDAMENTALS
** Get your JR PASS.** The only thing you need to do is estimate if you need a one week / two week pass. Some people recommend organizing your itinerary to save money on the pass (doing two ways Tokyo - Kyoto in a week). Don't let your need to save a couple of bucks make you rush on your pace. I ended up buying a 7 Days Pass and buying a one way Shinkanzen ticket for the day it wasn't covered by it. I ordered the pass online and received it at home in 2 days. Once you get there, you exchange it for the real ticket and you are done. Seamless experience. There are sites that let you 'Calculate' which pass to buy based on your itinerary.
** Wifi Modem:** Life saver. It was really easy to have my pocket size modem in my backpack and have unlimited internet. I payed 80 USD for 17 days. Received my modem on my hotel on arrival and returned it by post from the airport.
SMARTPHONE APPS: - Foursquare: I used it before the trip to make a list of places of interest! and restaurants I wanted to go. Once there it was really easy to see everything in a map. I didn't find a better app to do this. For reviews Yelp and Foursquare took me to great restaurants and bars.
Google Maps: Works perfectly to find places, to see how they look (some times are hard to find) and to get the times of the next subway.
Hyperdia: Great app to plan your itinerary on the Shinkanzen and other local transportations.
Google Translate: It is so easy to travel having this. I used to use the app with the camera to translate menu and signs in real time. Japanese were amazed of this too.
UNIQUE EXPERIENCES:
Sleep in a Ryokan: The typical japanese hotel experience. Amazing food. You walk with a Yukata around the hotel and sleep in a tatami. They use to have an Onsen too. Do it! I did it in Takayama.
Onsen: The thermal baths everybody are afraid of doing. So much relaxing and very unique experience. There are onsen parks, in hotels and towns. I recommend do it at Oedo Onsen in Tokyo. Then you will want' to do it everywhere.
Food: Everything is delicious. I recommend using the online recommendations to get to places you will love. The two places I went randomly weren't of my taste. On Foursquare you can get all the places you need. I didn't go to any fancy restaurant that needed 90 days prior reservations.
Festivals: Check online if during your stay there is any festival going on. I happened to be during Kanda Matsuri - that happens once every two years - and was a highlight.
WHAT I WOULD LOVE TO DO, BUT DIDN'T:
WEBSITES OF REFERENCE AND INSPIRATION: - Japonismo.com (spanish) - MuyLejano.com (spanish) - https://nerdnomads.com/ - japan-guide.com - https://www.reddit.com/r/JapanTravel/ - Eater Japan Guide
DESTINATIONS CONSIDERED BUT NOT DONE: We loved our trip. It felt very rush even with not many places. I wouldn't have added any other place. There are many places I considered but then decided not to go, and focus on a small numbers of cities/towns. - Hiroshima - Yokohama y Kamakura: We had enough city and temples with Kyoto and Tokyo. - Lake Kawaguchi: Close to Mt. Fuji. But required a big detour. I ended up staying a night in Hakone and saw Mt. Fuji from there.. Koyasan:Sleep in a Budhist temple. Kanazawa: I was between this and Takayama. Ended up choosing Takayama and it was a highlight.
** FINAL ITINERARY: ** - TOKIO: 5 nights - TAKAYAMA: 2 nights (Daytrips to Shirakawa-go) - KYOTO: 5 nights (Daytrips to Osaka, Nara) - HAKONE: 1 night. - TOKIO: 2 nights
Will talk about each place on a dedicated posts.