I just came across a japan-guide article about getting lodging in Kyoto during peak season:
http://www.japan-guide.com/news/0029.html

There was a recent post on this subject where I suggested a tour package from Japanican but was not sure how it worked.

The article confirms what I suspected about those packages:

<i>Tip 3 - Book as part of a package

<b>One reason why hotel vacancies get scarce in Kyoto is that tour companies reserve large blocks of hotel rooms to bundle them with transportation or admission tickets into tour packages.</b> <u>Japanican</u>, for example, offers hotel rooms as part of their Shinkansen Tour packages. While competitively priced, many of these tour packages are tied to train tickets and would not be ideal for Japan Rail Pass holders. </i>

I think a Japanese travel agent could help in any case and would be heading to a local H.I.S. Travel office (or other agent) if I couldn't find what I wanted.

And they seem awfully expensive, like 80,000 JPY for the days in November that janisj wanted....at least it seems expensive to me. ;-)

The rt fare on the Nozomi is about 28,000...

But a local Japanese TA might have something better...

I second the comment about using a Japanese travel agent. I recently tried to book accom in Kyoto right in the Osaka Sumo / cherry blossom season and could not get any decent accom. I spoke to a local travel agent, they could not find any accom either but then they rang Japan Travel Bureau and - bang! got the accom I wanted.

Available lodging at an expensive price might be better than no lodging at any price.

In my younger and poorer days many moons ago, having spent one night during a booked out holiday at the top of some stairs at the Kyoto railroad station practicing saying Urusai to our homeless companions, I second that thought.

Kyoto may be booked out but Nara is not--and in my opinion it's a more interesting and attractive destination. It does require research, however, as you need to explore further than the deer park.