You made me curious, GC3, and I had a look at their availability as a result. There are actually a few rooms available over that period still. There's a deluxe twin with ensuite that would cost a total of 41000 for 2nd, 3rd, 4th November (for 2 persons). The 3-bed private with ensuite would be 41100 for the same 3 nights. It's not the most budget, but for a private bathroom and non-Western accommodation it's not horribly priced. Surely there are more affordable places around....... okay, so now I've made myself curious. Ikoi-no-Ie Kyoto has a room with ensuite available all those nights, at 5500 yen total per night. If you didn't require an ensuite, your options are even greater and much cheaper. I was looking at Hostelworld.com by the way.
Also, with the night most of us have recommended you spend in Miyajima (or Hiroshima if you've got budget issues), may I suggest you don't do that at either end of the Kansai section of your trip. Stay in Kyoto (or a cheapie hotel in Osaka near Namba or Shinosaka station as Dick H has highlighted if it's just for the sake of a bed for a night) prior to heading to Chugoku, or the night you leave Chugoku. You don't want to spend a day travelling to/from Hiroshima/Miyajima to/from Tokyo.
How about Koyasan? It's stunning.
Here's an example of where it'd be nice to spend the nights, in my opinion:
2nd Kyoto
3rd Kyoto
4th Koyasan
5th Osaka
6th Miyajima (or Hiroshima)
7th Osaka
And without Koyasan:
2nd Kyoto
3rd Kyoto
4th Kyoto
5th Kyoto
6th Miyajima (or Hiroshima)
7th Osaka
Handy accommodation sites:
http://www.itcj.jp/eng/index.phphttp://www.japaneseguesthouses.com/index.htmhttp://www.shukubo.jp/eng/05_syukubo.htmlAlso, I re-read an earlier response. In terms of daytripping from Tokyo, don't drop Kamakura. It's so close to Tokyo, yet so different. If you go to Nikko, be aware that Edo Mura is really quite staged and more of a tourist attraction than an historical village. It's far from cheap, but if you like kitschy places, go for it. In terms of ninja's, we found the ninja museum at Iga Ueno to be more informative. It's a long way out of the way though.
We spent our honeymoon relaxing on a secluded island in Fiji for 10 days, but I'm sure envious of your plans! You'll have a brilliant time :)
Sorry for the word wall.