Do you mean go straight from NRT to Kyoto upon arrival? That would depend on when your flight arrives. If you get in fairly early in the day - say by mid-to late-afternoon, it can be done. It will just be pretty tiring after a long flight. If you are in J (I assume that is what we call C in United-land) you should be able to get some sleep on the flight over and so not be too wasted. Figure a couple of hours or so to negotiate C&I, collect any baggage, get some money, find the train station, purchase tickets (there WILL be a line) for the Narita Express and the shinkansen from Tokyo to Kyoto, wait for the next N'Ex and get on the train. If you will be using a Japan Rail Pass, there will be a few minutes involved in activating it, again after waiting in line. The ride to Tokyo Station is a bit under an hour. Then you need some time to navigate the huge Tokyo Station to the shinkansen platforms and wait for your train (do not let the ticket agent schedule you with a 5 minute connection in Tokyo - insist on at least 20, 30 is better for a first-timer). The ride to Kyoto takes about 2.5 hours if you do NOT use a JR Pass and just purchase Nozomi tickets. It is around 3 hours on the Hikari if you are using a Pass. Total actual transport time from the NRT train station to Kyoto Station = 3.75 to 4.5 hours not counting walking/waiting time. From plane to Kyoto, figure 5.5 hours if everything falls just right - more like 6 or even up to 7 in many cases.

The N'Ex averages twice per hour in the evenings. The evening Nozomis from Tokyo to Kyoto run several times per hour up until 9:20 pm. The Hikari (for Rail Pass users) stops running at about 8:00 pm.

The answer to your first question depends on whether you want to face 4 to 5 more hours of travel after your arrival.

I'll let others field the Hakone questions.

Give yourself at LEAST 2 hours at the airport before your departure. They actually suggest 3 hours but that is a bit much. I usually allow 2.5, but I am a bit obsessive about being early everywhere.

For a 14:55 departure, I'd plan on being ON the N'Ex from Tokyo by no later than noon, a little earlier from Shinagawa if you go from there.

I think you could depart for the airport directly from your last stopover point if you start fairly early in the morning. I went all the way from Shikoku Island to KIX the morning of my departure last fall. Just plan out the connections ahead of time to make sure of the times and have some backup connections just in case. Hyperdia is your friend: http://grace.hyperdia.com/cgi-english/hyperWeb.cgi . For most stations, just enter the city or station name. For NRT, use Narita Airport.

JR

For a 14:55 departure, if I am in biz class or have status on the airline, I would leave Tokyo at 12:40 myself and still have time for the airport lounge. Except at the start of Golden Week or something like that, I have never needed to be at the airport 2 hours in advance.

They recently improved the JR office traffic flow in terminal 1. There are two positions for tickets and pass exchange orders and a separate person just for the N'Ex/Suica deal.

I find the Hakone area rather touristy, but it's Japanese-tourist oriented, so you may find that interesting. You certainly can activate your pass and go to Kyoto on arrival. Since you are flying DL, you won't have cheap choices to fly domestically, train would be next best. I might be inclined to do Hiroshima/Miyajima a bit later in the trip, a day or two without long train travel might be nice on arrival.

Hi Everyone,

Thanks for all the suggestions so far. I've updated the itin from what I heard here and changed the initial thread.

Still trying to figure out Hakone as I'd like to visit the hot springs! Not sure if it'll be a Sunday AM train, check in, tour, enjoy the Rayokan and then get to bed. Then home in the AM or a Saturday afternoon type affair.

Any suggstions?

I appears that you're visiting Takayama. So you could extend your time in that area by an extra day - visit a hot spring in Oku Hida - and skip Hakone altogether.
http://wikitravel.org/en/Oku-Hida_Onsen_Villages

Wish I could but by then the 7 day rail pass would be over and I'd have to pay to get back to Tokyo on my own.

It is entirely possible to go from Tokyo to Hakone without riding a JR train.
You can ride the Odakyu 'RomanceCar' Limited Express from Shinjuku to Hakone-Yumoto for �2,020 {including the reservation fee} each way. The train is direct, and takes 85 minutes.
Or you can obtain a special two-day Hakone Freepass for �5,000. It also includes other local transportation services and provides discounts to area attractions.
If you're staying somewhere other than Shinjuku in Tokyo, use Hyperdia to add in the subway station where you originate.