2-week itinerary review

Hello all,
I'm going to Japan from 9/4/2010 to 9/17/2010. Can you please review my itinerary and let me know if something doesn't work?

9/4: Depart airport
9/5: Arrive at Narita, transfer to hotel in Shinjuku
9/6: Tokyo
9/7: Tokyo
9/8: Tokyo
9/9: Tokyo
9/10: Tokyo
9/11: Tokyo, activate 7-day JR Pass, take side trip, return to hotel in Tokyo
9/12: Side trip, return to hotel in Tokyo
9/13: Side trip, return to hotel in Tokyo
9/14: Check out of hotel, take bullet train to Kyoto, check into hotel in Kyoto
9/15: Kyoto
9/16: Kyoto
9/17: Check out of hotel around 11am, take bullet train to Narita (switch trains at Tokyo), flight at 6:45pm

We bought a package that requires us to return to Narita to take our flight back to the states. Should we worry about making our flight on time if we're traveling from Kyoto on the last day? Our travel agent suggested we fly from the Osaka airport to Narita but I thought it was a waste of $125+ tax when we could put it towards the 7-day rail pass and take side trips.

I'm worried about making our flight on the last day but I want to avoid checking in and out of so many hotels. We could also go to Kyoto on 9/11-9/14 and return to Tokyo on 9/14 to 9/17.

Thanks!

I see no problems.

I'm worried about making our flight on the last day but I want to avoid checking in and out of so many hotels.

Under normal circumstances it should be no problem. To be on the safe side, I would consider departing Kyoto even a little bit earlier. In unlikely case that the shinkansen is out of order, you could consider flying from Osaka's Itami Airport as an emergency meassure. There are many flights to Haneda Airport and a small number of flights directly to Narita Airport.

I'm worried about making our flight on the last day but I want to avoid checking in and out of so many hotels

Agree with being based in one or 2 places and utilizing JR Pass: we do that as we have family in Tokyo and Osaka.
We always fly in and out of Narita, and the flight home usually leaves at 8pm.
I agree with Uji, I would leave Kyoto a little earlier, and change to Narita Express at Shinagawa: it is a MUCH MUCH easier transfer than at Tokyo station. We usually have about 15 mins between trains which is heaps; at Tokyo you'd walk much further and need much more time.
However, I can also recommend 2 nights in Kanazawa or Takayama, rather than all the time in Tokyo:
1 Nikko is easier on NON JR;
2 Kamakura is not expensive on JR.
3 Hakone is easier on NON JR
Just a thought. Enjoy!

I think your itinerary looks great, and i don't think you five days in Tokyo is too much!
Of course, that depends on your interests, but there is much to see and do in Tokyo! I can spend weeks there and never get bored.

But of course, if you are more interested in historical sights/atmosphere, places like Takayama and Kanazawa are better.

Thanks for the replies and the suggestions for side trips! We're not sure what we're going to do in Tokyo so we may spend less time there and more time doing our side trips.