Japan Dec.25-Jan.02 Tokyo, Kyoto, & ?

Hello All,
First, thank you very much for this website, all its valuable information, and all the people that contribute to us fellow travellers.
I have searched this forum looking for answers, and I have got some, but I would like to share our trip ideas, in hope of some advice. We are very confused as to where and when to go.
My wife and I are going to Japan arriving Tokyo Dec. 25, 2007 at 10am, leaving from Tokyo on Jan. 02, 2008 at 8pm. In our plans, we have Tokyo, Kyoto, and Hakone to visit. I really do not know if it is enough time to go to Osaka. Or if it is better to go to Osaka instead of Hakone. For what I�fve read here, the last week of the year is a little bit complicated; Shogatsu is the most important holiday of the year, so we are expecting difficulties. The questions are how to organize our trip:
1. I want to go to Akihabara, so I would think that it is best to stay in Tokyo the first 3 or 4 days, and then go to Kyoto, Hakone or Osaka. This is just base in the fact that I will suspect Akihabara to be close on the 30th, 31st, and 1st of January. Is this correct?
2. Then, we can go to Kyoto, stay there for 2 or 3 nights. On the way to Kyoto, we can stop in Hakone for one night.
3. Now, where is better to spend 31st Dec and 1st Jan, Tokyo, Kyoto, Osaka?
4. I have mentioned these three cities because of what I heard, but in fact we are not sure where to go and for how long. Any opinions for other cities and places to go are very welcome.
5. Options for length in each city are:
Tokyo = 3 days, Hakone = 1 day, Kyoto = 3, Tokyo = 1day. Or,
Tokyo = 3 days, Kyoto = 2 days, Osaka = 3, Tokyo =1 day. Or,
Tokyo = 3 days, Hakone =1 day, Kyoto = 2, Osaka = 3.
6. All the decisions are going to be base upon what attractions (and where) are closed because New Year.

Thank you for all your big help,

Kmilo & Caro.

It's a bit early to tell you what kinds of attraction is in place for New Year 2008. But you can use this page for your guide.
http://www.japan-guide.com/e/e2276.html

Akihabara is open on Dec 30/31st. Shops (especially small shops)may be closed on Jan 1st.

I personally like staying in Kyoto on Dec 31st to Jan 1st because it is a very special day and the city is full of energy. But I wonder if you can get a hotel there at this stage. Also it is better to stay away from Hakone on Jan 2/3 as the big marathon(ekiden) tournament is held there.

Thank you for your answer.
What we have at the moment is:
1. 25th-28th Dec. Tokyo, with either a day trip to Hakone, or instead of spending 28th on Tky, go to Hakone and spend one night. For Tky we'd probably have Shigetsu Ryokan. For Hakone, I've contacted Takaragawa Onsen, but I still not sure because it is a little bit high price for our budget.

2. Sun. 30th Dec - 2nd Jan 2008 in Kyoto, with a visit to Osaka on the 30th or 31st. Not sure about this because of the 31st might be difficult on traveling and attractions open in Osaka. Same for the 1st of Jan, and on the 2nd we will be heading back to Tokyo to take the plane.

Now, I would appreciate very much all the help w/ hotels, particulary in Kyoto. There is where we don't have yet a good recommended place to stay. Also in Hakone please!
Per Osaka, we decided with my wife to try to visit it in a one day trip having Kyoto as a base, so less hassle with hotels, bags, etc. Is this a good decision?
We hope with this itinerary we will have a good chance to have a taste of Japan without too much rush, that is why we are taking out Osaka as a stand alone place to visit.
Many thanks,
Kmilo & Caro.