Question 1
Christmas day is not a special day in Japan. Everyone is working both on the 24th and the 25th, unlike the 23rd - the Emperor's birthday - which is a bank holiday day. For this reason, there is no special good place to spend Christmas in Japan... except perhaps in places where there are many foreigners. I spent a Christmas in Hakuba, and this was real fun. But between Tokyo and Kyoto, there is no significant difference...
Question 2
Keep in mind that in winter, there is lot of snow in Kisoji. Walking between Magome to Tsumago might not be that interesting in that season, even if visiting those towns is probably well-worth. Same goes for Noto Hanto, in winter, the visits might be rather limited.
Question 3
Kuroneko is what you are looking for. They have offices in every airport.
link :
www.kuronekoyamato.co.jp