Thank you both so much! In fact, thank you doesn't even begin to cover how grateful I am for such amazing answers. This is exactly what I was looking for; organization and suggestions on what to cut. And the best part - the hidden gems you both offered. They all sound perfect and are now on the list.
Abmj-jr, you are a gem, one of the shining stars of this board with all the help and advice you offer to everyone who asks. You are right; Jedai Matsui is on the 22nd, Wednesday. We left Wednesday free just to experience it. I love the suggestions for markets, strolls, shopping etc. Exactly was I was hoping to get.
And LapLap, thank you as well. You are amazingly helpful. Exactly what I was looking for and you are right - not a single museum other than Yasukini. I don't know why, as I love museums. So I'll have to re-look at that and any suggestions in Tokyo are most welcome. But all the other stuff is perfect, especially the suggestion of Tokyo Int'l Forum and YaNeSen.