Hi Bruno,
Great to hear you are pulling all the pieces together - your trip looks great!
Based on your new itinerary I think I would recommend a 14 day rail pass. As the ticket costs for Tokyo <> Nikko + Tokyo <> Kamakura is ¥14,660, this would make the costs for a 7 day pass + separate tickets ¥47,150 (¥28,300 + ¥14,660 + ¥1450 + ¥2740). As a 14 day rail pass is ¥45,100, you'd be better off going for this option with these new additions I think. Taking the Nikko trip out, it's clearer to go for the 7 day + separate tickets depending on how flexible you want to be around Tokyo.
Can I use the JR Pass to commute between Osaka and Kyoto? I could not find hotels in Kyoto and we will need to sleep in Osaka, close to the Shin-Osaka station, and commute from there.
Yes this will be fine - in fact it's a great idea as hotels in Kyoto can be pretty pricey!
Any recommendations on the passes for Tokyo? Especially if I want to go to Nikko (maybe) and Kamakura (for sure)? Would the PASMO card be the best option? Would it include the Nikko, Kamakura and Narita tickets or I still need to buy those separetely?
If you have the JR Pass you'll find this map of JR stations and trains useful as these can be used for free. If not, a Suica or Pasmo will be versatile as they can be used on JR East trains (including the ones you list) as well as the metro. Here's a blog post with more information on the differences between these two cards. Please note that Pasmo and Suica are prepaid cards and do not offer any real benefits over paying with cash/credit card at time of travel except convenience.
As I mention above, if you do decide to go to Nikko, I very much recommend the 14 day japan rail pass over the 7 day.
For Hakone, the JR Pass will take you as far as Odawara. From Odawara you will need to use the Odakyu Hakone Railway system to get up to Hakone as it is not a JR operated line. Odakyu sells a 2 and 3 day pass that covers travel up and around Hakone that you can purchase at Odawara. You can find out more on the Hakone free pass here.
Hope this helps!
P.S. I calculated the full costs for your itinerary again as it had changed quite a bit. For reference, here it is:
- Narita airport terminal 1 > Hiroshima: ¥20340, (378mins, 973km)
- Hiroshima > Osaka: ¥10520, (109mins, 345km)
- Osaka > Kyoto: ¥540, (29mins, 42km)
- Kyoto > Osaka: ¥1680, (27mins, 42km)
- Osaka > Kyoto: ¥540, (29mins, 42km)
- Kyoto > Nara: ¥690, (44mins, 41km)
- Nara > Osaka: ¥780, (55mins, 48km)
- Osaka > Kyoto: ¥540, (29mins, 42km)
- Kyoto > Himeji: ¥5130, (62mins, 130km)
- Himeji > Osaka: ¥1450, (61mins, 87km)
- Osaka > Odawara: ¥12270, (158mins, 472km)
- Odawara > Tokyo: ¥1450, (36mins, 83km)
- Tokyo > Nikko: ¥5430, (121mins, 150km)
- Nikko > Tokyo: ¥5430, (117mins, 150km)
- Tokyo > Kamakura: ¥1900, (47mins, 51km)
- Kamakura > Tokyo: ¥890, (54mins, 53km)
- Tokyo > Narita airport terminal 1: ¥2940, (58mins, 79km)
TOTAL: ¥72520 for 17 legs