My man spent five years in Japan... that's why he doesn't want to accompany me, he stayed there too long ^^' But I am sure I will go one day. Wanna see the country that produced so many things I find mesmerizing and beautiful.
Forgive me if i am posting info that people already know, i didnt see it in the thread so figured it was better to post detailed info rather than 'yea ive been there' type info.
I think the biggest thing you should learn right away is how to use the rail system; With the visitor pass you can ride the JR lines for that region for free including some shinkansen routes (riding a 250mph train is fun); They are regionalized, so you will want a good plan for how you want to schedule your visit, you dont want to say 'i feel like seafood' and want to hop the shinkansen to Hokkido only to realize thats part of JR north and has its own Pass; Also it doesnt include things like subways (Tokyo) or the trolleys; so its good to always have money on you. The freedom the rail gives you in Japan is 2nd to none, completely different than here in the states. On a whim you can change plans and go somewhere completely different with little to no difficulty at all. Everything is in english/romanji and there are maps everywhere. You might find that you get there and the weather is going to be horrible and might decide to just jump a train to another city where it wont be as bad or has more indoor activities, so while its nice to have a list of things to do, its not a great idea to have a 'specific' itinerary.
In general the people were very nice, but dont expect a lot of help in the English department. I was completely lost on how to 'get' to the shinkansen tracks (for the shinkansen its like a terminal in the terminal and at least in Osaka looked like a exit, so kept missing it) so i kept asking and people just looked at me. I ended up missing the train and went to the the ticketing areas to get a new ticket; They looked at me and shook there head and said 'stanby only, punishment for missing your train'. I still couldnt get anyone to tell me where the platform was and I ended up giving up and taking the local which was about a 2 hour ride (super crowded) vs 10 mins. Also for every trip on the JR you need to go to the ticket office first and get a ticket. All you have to say is the time and your destination and show the pass, they will print it for you, you cant use the terminals with the pass and tickets can be expensive. Also leave extra time like going to the airport, some of those lines can take a hour to get a ticket.
Speaking of travel, pack in a way that you can utilize the lockers at the train station. Since you will probably be on the move at all times and might not know what city you will end up in, its great to just take all your luggage and shove it into a locker, then come back later to get it; Especially if you plan on going for weeks; This way you can just have a overnight backpack that you keep with you (which is also great if you get caught by a unexpected rain storm and get drenched) and the majority of your stuff in a locker, not having to hauling it around the country. Since the rail system is so good, its not hard to pick a central train station like Nagoya or Osaka since you will probably be catching a connecting line at one of those stations and use that as a base of operations.
If possible open a bank account with a bank that has branches both here in the US and over in Japan. This way you can use the ATM's for free and avoid foreign transaction fees. If they also happen to have branches in the city you are in, then at the end of the trip you can simply deposit the left over money back into your account and avoid the conversion fees. I was able to do this with citi bank while i was in russia, it made things way more convenient. In Japan there is also citibank, but only a few branches and by the time i got there they were closed, and the ATM didnt work at the airport, so its hit or miss there. You might have to plan a trip the the bank in order to make things work out. If you try to convert the money back here in the US you will get hit with like 20% fees; You could also use credit cards, but they are not as popular over there as they are here, so be prepared to have some cash at all times.
I think the thing that stood out the most was how quiet people were on the train. You would think that a group of people would have conversations, but no, its like being at the library. No one talked, everyone was dialed into their cell phones. Its amazing to watch people completely passed out on the train sleeping, and then the little tune goes off for their station (every station has its own little song that plays on the train when you arrive) and poof they are up and ready to go like someone flipped on a light switch.
All in all, its nothing like anime, so get that out of your head right away; Anime is a hyperbole of real life there and should be treated as such; That being said, i can say for certain that out of all the places I have been in the world, Japan is the one i would return to. As a history buff, I was only there for 2 weeks and feel i needed another month to get in everything i wanted to do, even then there are places i have seen and would still want to revisit.