This is a really great guide to someone visiting.
The only two things I would add are:
Walking, while it is great to take the trains to get to places in and around Tokyo, it is also a good idea to walk around a bit and explore the hole in the wall spots. Many places have at least one person that will try and help you in English. It may not be the best or most fluent English, but some of my best meals in Tokyo have come from following my nose and I (have dietary restrictions and) speak virtually no Japanese. Patience is key.
Also, while the Western Brands we know are reliable, I suggest trying any of the Prince Hotels (http://www.princehotels.com). When I first visited Japan, I stayed at the Grand Prince Takanawa, and I now live here. Also, try a capsule hotel — just for one night — for the experience. They are an interesting adventure. If you are intimidated by the original style, you can try out a milder version with First Cabin, which feels like your own room but isn’t quite that. Japanese lodgings can be fun if you take your time to find the fun options like Temple lodgings or Ryokan.
No matter what, throw away any pre-concepts of what Japan is like, and come for the adventure and fascination of something unlike the life we’ve lived. If you are here for a long enough time, come visit Tohoku, that’s where I live :)