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Japan Itinerary & Logistics - help, feeling frantic!

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Hi All,
My trip to Japan is coming up in 19 days and I'm trying to figure out right now a few things:

1. Should I purchase a JR Rail Pass?
When I estimate costs for using the JR rail to get between my itinerary destinations, the total amount is coming in around $250 whereas the rail pass is $276. Seems like I should just purchase tickets one by one when I'm there. But, am I missing something? Everyone says what a good deal the JR Rail Pass is.

2. Should I purchase day trip tours for top tourist destinations?
See my intinerary and add'l questions listed below.

3. Do you think I should skip something on my itinerary in favor of Koyasan or another stop? Just curious because if I'm making any changes it needs to be now.

Here's my itinerary:

4 nights here getting in late Thurs. evening, spending Fri. enjoying the Sanji Matsuri festival, Sat. touring about Tokyo, Sun. day trip to Nikko, Mon. Akihibara in the morning and leaving for Kyoto in the early afternoon.

Travel = Tokyo to Nikko roundtrip; Tokyo to Kyoto one-way.

Add'l Question = Should I purchase a day trip tour of Nikko from The cost is $125/person. Do you think we could easily understand what we are seeing and get around ourselves? I'd rather do that, but I don't want to miss getting the full experience.

3 nights here. Monday afternoon touring Gion and taking in a geisha show. Tuesday tour temples/shrines, trip to Nara?. Wednesday Arashiyama bamboo forest and monkey park. Gion tea ceremony maybe. Thursday morning depart for Shimoda and spend one night at beachside ryokan there before returning to Tokyo to leave.

Travel = Kyoto to Nara roundtrip; Kyoto station to Arashiyama roundtrip; Kyoto to Shimoda; Shimoda to Tokyo.

Add'l question = Should I book a tour on to take us to Kyoto hot spots in the morning and then to Nara for the afternoon? It costs $134/person. I'm wondering how easy it is to get to the tourist destinations (e.g. are they in walking distance in Kyoto?) and if we'll be able to really understand what we are seeing without insight from a guide. Worth the money or DIY?

I so, so, so appreciate your advice and insight! I'm feeling kind of frantic to get things all planned out now that the date is coming up so quickly.

2. If I should purchase day trip tours to tourist destinations

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