I love this place! We've been here 10 days now and are sad to be leaving soon. I thought I'd write a brief travelog with some tips for other first time visitors.
Arriving at NRT was a bit of a PITA as there are no express lines for C/F and we came in just after another jet. But the total wait at immigration was only 20m so not as bad as LHR and others, and our checked bag was waiting as we exited. The NRT express train is super easy to find - almost directly across from customs exit. Easy to buy tix with CC (and a steal at 1500 yen pp) and the girl can direct you to 7/11 and Citi ATMs which are just around the corner (both accept US ATM cards). Finding the train is a slight challenge you have to go downstairs and then follow signs to the correct track.
The train itself is nicer than HEX (London) but much longer ride at 80 minutes to Shinjuku. Arriving in Shinjuku at rush hour was not as bad as we expected - yes crowded but not crazy. Finding a street exit takes a little time but once you do so taxis are easy to find. There is a shuttle to the park Hyatt but not so easy to find and a bit of a hassle if you have significant luggage. But we used it often when going and coming during the day.
The Park Hyatt itself is everything that you expect in terms of luxury and service. I have stayed in bigger and more deluxe rooms, but for Tokyo it is hard to beat. The staff was uniformly good (aside from a situation at the Peaks bar that I will address elsewhere and was satisfactorily resolved). The location is a bit further from Shinjuku stn than one would like but worth the walk or quick shuttle or taxi.
The first night we went back out to eat in the area between the hotel and trains, there are many restaurants on the small walking streets. We found one with the sushi boats and stuffed ourselves for $40. Good fresh fish which hit the spot after airplane food. Second night we got tired and basically made a meal with the Peaks lounge hhour appetizers. Third night we went to Gonpachi in Roppongi, a great experience and quite reasonably priced. The final night we did not feel like walking so we descended into the basement of the office building under the Hyatt which like most offices has many restaurants plus convenience store, drugstore (needed suntan lotion!) Just walked into a sushi bar that looked nice and enjoyed a great meal with sake for @ $80. There are probably places like this everywhere in Tokyo if you are willing to roll the dice and explore outside the guidebook and concierge high end lists.
We spent our first two days full days with two wonderful gentlemen provided by tokyofreeguide.com. We were fortunate to get 2 separate tours (apparently I made 2 requests) and I cannot say enough great things about these guys. They each split up the major sites - met us at our hotel at 9am and then directed us back at 5pm with the only cost for their metro fares and modest lunch. Better than any tour bus and great exercise. My only caveat would be to prepare for a lot of walking through parks to see shrines, etc. - if this is not your thing then maybe better to do something else. The river boat cruise was a nice interlude and we ended day one at the Akihabara electronics area. The fish market puts my own SF fisherman's wharf to shame!
The final full day in Tokyo we took a day trip to Kamikura which was one of the highlights of our trip. Yes, it's touristy but a pleasant change from the hustle of Tokyo and some great shrines and the giant Buddha. Time well spent if you have an extra day though finding the right train there was not easy (in part due to some service issues which required connecting in Yokohama).
The next day we took the "Romance Car" train to Hakone. It is not so easy to find the right tracks, you basically have to go to the far North? part of the station, almost through a dept store to find the train. The ride is about an hour, nothing special - I would not pay extra for this experience again.
My least favorite experience of the entire trip was spending a night in Hakone. The train itself was pleasant, but I could do without the 1/2hr ride on the curvy road to the Hyatt in Odawara. Honestly the communal onsen baths just did not appeal and in fact made me nauseus (maybe too hot) plus I prefer to enjoy a hot tub with my wife and not some naked old men

We considered a ryokan but the lack of private bathroom at most was a nonstarter not to mention the prices. It did not help that I felt ripped off at the nearby Nobu restaurant which was nothing like the wonderful experience we had in London. While we did enjoy taking the tram to the nearby hot springs (and great views of Mt. Fuji) I felt the whole experience was a bit overrated, way overpriced, and definitely not worth a diversion from much more interesting places.
We had no trouble buying Shinkansen tickets to Kyoto at the JR counter and finding our car. Very pleasant way to travel and 2 hours later we were in the heart of Kyoto. Once again Kyoto station is not the easiest to navigate but the guy from the information booth personally escorted us to the Westin shuttle stop (several people did this throughout our trip - an amazing kindness that you don't find elsewhere). Alas the Westin Kyoto was a big disappointment - my fault for not reading the reviews more closely and for being penny wise, pound foolish. Considering the perks we get at Hyatt, that would have been a far better choice. See my review in SPG forum for more details.
Part II - Kyoto and Osaka coming soon. Apologies for spelling errors