This advice goes back about 4 years so I can't guarantee the accuracy of prices. Think about the bullet train trip and how many you plan to do. When I went I took 2 trips - one to Osaka south of Tokyo and another to somewhere north. They cost about £90 each. Yes, it's expensive. However, you can get a JR railcard at around £140 for the period that I wanted, I think it was 9 days. My memory's not clear on this but I think they sell them in blocks of maybe 7 days, so it may be less than £140 for you. You can use it as many times as you like, so 2 trips or more on a bullet and you've saved money. Remember - these are old prices. It does not allow you to travel on the one maglev bullet train though. Tokyo has 2 rail systems, one of them being JR and you can use the card for unlimited travel on this. You can only buy this JR card from a Japanese tourist office here in London. You cannot get it out there. The bullet train is unbelievably punctual - almost to the second. It's probably a life jail sentence to make it late. Passing through some towns you are travelling at something like 180 mph about 5 or 6 feet away from peoples home windows.
The JR network is mostly overground with some underground. The other network is the opposite. regardless, you'll be using them both. With the JR card you show it to a ticket man at entry/exit gates. With the other network you'll have to hunt round for ticket machines with English on them. Get an all day ticket for about £4.50. If you have difficulty the locals are very helpful, especially the young ones. The JR card will also get you to and from the airport - normal price something like £15 each way, I think.
You will be shocked at how little English is understood and spoken. I know we shouldn't expect them to be fluent, but considering the amount of written English you will see around, advertising, and their advanced technology, I had imagined they would be more conversant. Unfortunately I came up against a brick wall a number of times. The sales people in Akihibara get by ok but still not that good. As for eating, then you're on your own. No English, no pictures, nothing. At one department store cafe I couldn't even explain/indicate/mime/point to/whatever for a can of coke. If I ever go again then I'm going to take with me a set of picture cards with chicken, cow, pigs, drinks etc on them. In my 10 days there I ate almost nothing but McD and KFC where they had menus with pictures. Prepare to be shocked to find that they are all smoking restaurants - no segregation even.
One place to visit is Tokyo Tower which looks like the Eiffel tower. Some great views. Go up in the afternoon for day shots and wait up there until dark for night shots.
Akihibara will take a good couple of days - so many shops, and an indoor place resembling a rabbit warren of little market stalls selling every item imaginable.
Ueno park is ok to wander around. Some temples, a zoo and people watching. Fuji is difficult to make your own way to and view successfully. There is one place I found that gives a view from a distance that I found by chance. I'd suggest finding an organised tour to get there. Have a look inside the Sony centre and play with everything that they make.
Contrary to popular belief I did not find Tokyo to be the most expensive city in the world. My rooms on the 2 times I've been there were around £30 a night. Small rooms but more than adequate. I think I found them on either Expedia, Ebookers, or Totalstay. They were also away from the centre in the Asakusa district, but close to the underground. Asakusa also has one of the biggest most revered temples. I'm not a temple person and this one was just down the road. Nevertheless it was interesting. Food prices were similar to here. An all day unlimited underground travel card was about £4.50. If you take a taxi, then watch out for the door being opened mechanically by the driver.
Toilets. You may come across their traditional hole in the floor types but you'll find an abundance of western style thankfully. You may even find one that has a heated seat, music and other gadgets. And somewhere there is a restaurant with urinals hung on a glass wall with a view out on to the outside - albeit from a good height.
That's all off the top of my head.
