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Japan-Itinerary and transport questions-Help kindly requested!

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Good Day everyone! I am about 3 weeks out from my travel to Japan and have been doing lots of researching. Unfortunately, I've been too worried to actually book something at this point because I think I may be missing some of the fine (important) details of transportation. I have purchases the Japan by Rail guidebook which should get here tomorrow! *fingers crossed*

1. Cost is a factor but then again so is time as we arrive on Friday evening (may 30) to NRT and leave on June 12th out of KIX.

30th-overnight in Tokyo (thinking of staying in Shinjuku)
31-tokyo
1-tokyo
2-tokyo (Nikko day trip)
3-tokyo
4 leave Tokyo early, overnight in hakone
5 Leave hakone--(if traveling on JR pass-Come back to tokyo and take a bullet to kyoto because it seems faster per Hyperdia.com than traveling from Hakkone directly to Kyoto(?), overnight Kyoto)
6 -kyoto
7-kyoto--uji-nara (I know this may be rushing things, but I'm okay with this for the moment)
8-kyoto
9-kyoto
10 Leave Kyoto early (5:45am train) for hiroshima day trip on bullet (Leave luggage at Shin-Osaka station or drop off at Skin-Osaka station hotel) , return to shin-osaka-overnight
11 wake up early and take train from shin-osaka to mt koya, overnight.
12- Wake up and take train to KIX,Fly out of KIX (4pm flight)

Having said all of this, does this seem reasonable? I am looking to save costs on transport--does anyone have any insight on which combination of rail passes would make sense? I am willing to change my itinerary if something makes more sense for ease of travel and cost.

Nikko day pass, worth it?
Hakkone area pass?
Tokyo subway pass?
JR pass( 7 day)? I am aware of the limitations (no Nonzomi, liner trains etc)
Kansai thru pass? If not then a kyoto metro pass?


Thank you to everyone taking their time out to help me and hopefully others with the same question!

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