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Planes, Trains and Automobiles in Japan - Looking for Guidance

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I've seen a number of threads recently with recommendations and links to various websites regarding trains, etc. So I thought I'd see what the experts have to say about our situation. Here are my thoughts so far:

1. We have a tentative reservation at the Citadines Shinjuku in Tokyo and have some other options in the works. We will be traveling with several bags so the train will not be ideal. My understanding is that there is a limo bus that can take us from Narita to our hotel or, in the case of the Citadines, to Shinjuku train station where we can get a taxi to the hotel. Any comments?

2. After Tokyo, we are flying to the Noto Airport (NTQ) from Haneda (HND) on ANA where we will rent a car. We will be traveling light as our bags will be forwarded to Kanazawa. Our flight leaves at 10 AM. What is the best way to get to HND from Tokyo?

3. Also, we have not purchased the HND-NTQ flight as I know there are discounts etc. available - what are our options?

4. We will drive from the Noto Peninsula to Kanazawa and drop the rental car off there which should be "interesting". While we will likely have Japanese GPS and Google Maps print outs, does anyone have suggestions for reaching Kanazawa successfully?

5. Our next stop is Yamashiro Onsen (Beniya Mukayu) 25 minutes via JR train. We will forward our bags to Kyoto. Instructions on the ryokan's English website are fairly detailed, so getting to Beniya Mukayu should be no problem.

6. To Kyoto, 1 hr 50 min direct from Yamashiro by JR train. We are staying at the Hyatt Regency. Any suggestions?

7. We'll do a day trip (most likely) to Nara from Kyoto. Is this JR also?

8. From a previous recommendation, we will take MK Taxi to Osaka (ITM) from the Hyatt Regency for our connecting flight to NRT.

9. We have 4 nights Tokyo, 1 night Noto Peninsula, 3 nights Kanazawa, 1 night Yamashiro Onsen, and 5 nights Kyoto. What is the thinking on the Japan Rail Pass - can we get by on a 7-day pass? Are the subway systems in the various cities separate from this?

Thanks in advance for your help.

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