Fushimi Inari Shrine, Kyoto
Getting around Tokyo is super easy. All signage and the interfaces on screen based ticket machines are in English. Rather than buying individual journey tickets each trip (around 160 yen) get yourself a Plasmo card at the first Metro station you come to. They work on the Metro, JR lines in Tokyo and many food vending machines.
THE REST OF JAPAN:
A JR rail pass may be your best option if you are exploring outside Tokyo. It saves you booking a ticket for each journey and if you intend on going any further than a return trip to Kyoto, it will work out cheaper and give you an excuse to go somewhere else you weren't planning to go to.
It is worth reserving seats if you are doing a number of journeys, particularly during peak time (morning, arvo, weekends). You can do this at the english speaking JR offices where you swap your prepaid voucher for the official rail pass when you get to Japan. I usually go to the office at Ueno Station.
Note: You have to purchase the pass before you get to Japan as it is only for international visitors!
Tokyo is amazing. Have I said that too many times yet? I actually left this section until last as I wasn't quite sure where to start!
If you've never been then I highly recommend contacting the Tokyo Free Guide service. It's free because you are helping them practice their english skills. They just ask that you pay for their train tickets and it's probably nice to shout lunch!
Andon Ryokan is my first choice for any visit and I have sent many friends there who have loved it also. I first stayed there because it was so much cheaper than a 'western' hotel and well, looked fantastic. Since then a number of hostels have popped up (mostly in Asakusa) which could be a touch cheaper if budget is an issue.... but seriously, you will love the experience at Andon. Their breakfast is fantastic and they have a decent bottom-less coffee machine (decent for Japan!).
Kimi Ryokan also looks good as a backup – some sort of F1 pun? K's House which I will mention for Kyoto, now also has a hostel in Tokyo.