Tokyo was amazing Sk1pper. We actually changed the plan for the last 3 days so that we sent more time there at the end of the trip as the three days at the start wasn't enough.
I would have loved to go to Fuji but we just didn't have time - I'm sure that will be lovely.
There really were no issues with language at all. We were prepared to find it tricky in the big cities and tough in the more remote places but English was on all the signs and spoken by everyone we came into contact with. It was all just really easy!
The train stations can be a bit overwhelming to start with, especially when you've just arrived and are tired, but that's due to the sheer volume of people everywhere and the number of lines/platforms.
There are maps with the station names written in Romanji (i.e. using our alphabet) and if you're ever stuck for where to go/what ticket to buy you can ask any of the many, many staff that are around and they'll be able to help you in English. But you probably won't need to because everything's signed and all the announcements on platforms/trains/busses are done in English.
We went out there not knowing any words and have only come back with 'thank you very much' - to our shame!
Honestly, it all works so well and is so visitor friendly that you won't have any problems. They are hosting the 2020 Olympics so I think a lot of investment has been made because of that.
One of the best things is the number of public toilets everywhere. You never need to hold on for more than five minutes out there, it's bliss! Everything is spotless too and very, very safe. We never saw a single bike locked up in any of the cities, there is just no theft.
It's much cheaper than I was expecting as well. Out hotels were fairly expensive, but we went for nice ones and booked them late in the day, but restaurants, travel, shops, attractions etc. were all loads cheaper than over here. You can easily eat for under 1000 Yen (just over £7) if you go to local places, and the food is delicious.
One thing I would recommend would be to get a Japanese SIM or mobile WiFi if you want to avoid using your data overseas. There is WiFi around, but when you're travelling it's tricky to get onto the public networks (you have to pre-register and it's a bit faffy).
There is this article on TripAdvisor about some options.
You will have a brilliant time - when are you going? Just be prepared for it to be very busy!! And don't bother learning how to say sorry or excuse me when navigating through crowds, because no-one else does!!
I'm envious... I want to go back!