Hmm, more than a few suggestions, though I am not sure if you can see much if you are travelling to and from Kyoto or Tokyo so much. Many hours lost in travel, since many of the places you want to visit are a fair way away:

- Kyoto - a day trip to Nara (start early morning, can rush to get see the main sights in a day - beware deer poo). Kyoto's bullet train station is an architectural marvel in itself. Also some of the famous gardens.

- Kanazawa is a great little town, with an impressive station. I'd say 3 nights here. The Kenrokuen gardens are impressive, and the old quarter is very well preserved. It's also the home of the gold leaf industry, where you can get very shiny things for a good price. Getting gold leaf soap or sake as present is very novel. Personally I love the lacquered pieces with some gold leaf decoration. There are at lest 2 gold leaf manufactures (with short tours and freebies - check out the amazingly shiny bathrooms), and they have a very large selection of stuff. I wish I had bought more. We also went on a tour of the "ninja temple" with its weird assortment of false doors and traps, and a sake brewery. It does take a while to get to by train (2hrs+???) relative to the distance, since it's slow trains for a looong stretch.

- Miyajima is well worth the visit, in fact a whole day, and even a stay overnight. Beware the feral deer and monkeys. We spent our Hiroshima day here, and only got to see the A-bomb memorial at night. A rather haunting place.

- Hakone is a lovely area. Cruising Lake Ashi in a gaudy "pirate ship" (yes, think Pirates of the Caribbean) was a rather surreal experience. From various parts around there you can see Fujisan, weather depending. You can also boil yourself and simultaneously fascinate the locals when nekkid. I'd say stay 2-3 nights here.

BTW, the bus ride from Lake Ashi back to Hakone-Yumoto was the scariest trip I have ever taken in a motor vehicle. Worse even than the hoon in a minibus through heavy Beijing traffic to the airport for a flight we were late for. I was glad that I go climbing, as I needed the muscle to hang on and avoid being squashed against the other passengers, who were plastered against the windows.

- learn at least the Japanese words for left, right, straight, and station. And you may have noticed that their spoken English, despite years of study, is poor, but their written English is much better - you may communicate better by writing.

- JR passes are fantastic, if a bit primitive (just cardboard and a hologram sticker) but saved us heaps. JR even run some buses.

- have you stayed in a traditional ryokan? If only for a few nights, it's a real experience. They can be ridiculously expensive however.

- I find it funny that some ATMs have opening hours and are sometimes not open on weekends. Cash is good, even some hotels/motels/ryokans don't take cards.

- I nearly had a heart attack when, half asleep during a winter night toilet run, the toilet talked to me and opened the dunny lid itself. At least the seat was nice and warm.

- Oh, and you can get a little book at temples (Buddhist), or was it shrines (Shinto) where you can get someone at each temple/shrine to put the stamp of the place and some calligraphy in your book for a few dollars. I can't read any of it, but it looks impressive.

Essential Sites:
Want to know how to get to places, the cost, and how long it'll take?

and this one too

Goodwill Guides
I would highly recommend arranging for a goodwill guide for at least a day in each place you're going to. Generally you only need to feed them, pay for their entry to things (sometimes they can get in free), and sometimes their transport costs. A real bargain. You can contact the local group, specifying what language(s) you speak, when you are there, and what you want to see, and they will try and find someone who speaks at least some of your language. We found them very friendly and helpful. It's a great opportunity to learn more about Japan from a local, and they are very helpful with all sorts of things (where can I buy ___?). We brought along small gifts for ours (eg tourist special mini koalas, which they loved).

Anyway, you should have a great time. My links are nearly 4 years old, but I did collect lots of them if you're interested.

Maybe we need a Travel subforum?