The round trip N-EX return must be used within 14 days though, doesn't it? We will be using it for a return, but we are traveling for more than two weeks so I think we will need to purchase each trip separately.

Correct, Runner123 was doing five nights in Kyoto + one in Tokyo which is less than 14.

For trips longer than 14 days definitely consider alternatives (i.e., limousine buses or Keisei services) which can be cheaper and/or more convenient than NEx. And if Tokyo is only an interchange and not your first stop, then sometimes a domestic flight from NRT to your first destination in Japan can also be a good option.

Do you think I am better off flying to Osaka instead? There are flights at 5:30 and 6:20. The flight at 5:30 is on ANA itself, and right now is $87. Of course I then need to go on to Kyoto. Or stick to the original plan and take the train? If so, do I need to buy my Marita Express ticket now or can I wait for that too? If I buy it now, is three hours a good window? I will have the code for QR set, and only 1piece of luggage. Thanks for all your help. It would have been easier, I see, had I been staying in Tokyo overnight. But I leave home January 11. This is part of an ANA RTW ticket with a 2 week cruise from Singapore to Hong Kong in the middle.

which osaka, kix or itm

The train might get you to Kyoto a little sooner, but flying is cheaper. I think it comes down to what you are more comfortable with. Since you appear to have reservations about traveling without reservations, I suggest you fly.

17:30 flight with ANA is your best option - You have enough time for the connection. After immigration and customs, make your way to the domestic area of the terminal to check bags and go through security (T1 South). Don't go through security too early. There is little to do in the domestic gate area.

From NRT, ANA and JAL fly to ITM.

Flying is cheaper and I think they end up taking about the same time door to door. At ITM (ANA/JAL only fly NRT-ITM; NRT-KIX is LCC territory) you can catch a bus to Kyoto.

Depending on how important saving money is to you, the 6:20pm JAL flight can often be had for closer to $50-$60 if bought as a "Japan Explorer Pass" fare but of course it involves more hassle at NRT itself to change terminals.

It seems like flying the 6:20 JAL flight to ITM and then taking the bus is way to go. That flight is around $70, and I am fine with that. Then I can just buy the bullet train back as I don't have to worry about clearing customs. Thanks for all the advice!

FWIW - ANA also has promotional fares which may be worth looking into:
https://www.ana.co.jp/en/ph/plan-boo...special-fares/
Flying JAL will require a change of terminal at NRT, which is not a big deal, but worth noting.

Friendly note that I see it for $57 on Jan 11 & 12 (please be mindful of any differences in change/refund restrictions etc.): https://www.jal.co.jp/world/en/world...r/reservation/

Arrived at NRT on 24 Nov.
Long queue for manual Customs processing.
Walked right 50 metres to the area for scanning Customs QR codes. No queue at all, several people waiting to assist me. I used a manual print out and was landside in 10 seconds.
Using a QR code is the best way to go!
NOTE: Just to clarify, this was a JAL flight so landed at T2. Many other international flights land at T1.

landed this evening at 1635 JST, at gate 1650 JST

no line at immigration
no line at customs

out of airport down to train station at 1702 JST. very speedy day today

We are arriving 06:40 from Mexico into NRT T1. I hear a lot about the afternoon bank of flights and the long lines. How is it in the AM? Looking at FlightAware there are about 14 flights arriving between 6-7 AM. We have to hightail it to HND and have about 4 hours, the only concern I have is immigration as we will just have carryons.

Not too bad, it is one of the early flights. And with the 14 or so flights arriving during 6 to 7am they are spread across terminals 1-3. So not that bad in terms of crowding, though of course staffing does also reflect this.

Got to the arrival immigration area exactly at around 3:30pm today. Took 57 minutes to wait in line and get past just the immigration. This may be the longest it’s taken me ever.
They had the queue snake around very creatively, using every square meter of the available space to accommodate the volume of arriving visitors.