itinerary for 9 days in december?

I will be arriving in Tokyo on Dec 26 noon, and leaving the next year Jan 24 early morning. with a 1 week JR pass, which places do you guys recommend to visit? In chronological order, please. thanks.

Depends on your interests!

Some ideas:
http://www.japan-guide.com/e/e623a.html

Some suggested itineraries:
http://www.japan-guide.com/e/e2400.html

thanks for your reply. i have another question:

are all the shops, stores, restaurants in japan closed from december 28 to january 1?

Some are, others aren't. It's probable you can still buy foods and drinks. But not sure about clothes or electronics.

are all the shops, stores, restaurants in japan closed from december 28 to january 1?

No, most are open most of the days, except on January 1, when many are closed, but some are open:
http://www.japan-guide.com/e/e2276.html