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Need help, very overwhelmed with train lines and itinerary


My girlfriend and I are going to Japan this coming Thursday. We will be there for 16 days and already have our whole trip booked in terms of hotels. I am unsure if we need to get a pass out not. Here is our itinerary in terms of train travel, can anyone advise?

Day 1 - Narita Airport to Tokyo
Day 3 - Tokyo to Nozawa Onsen
Day 8 - Nozawa Onsen to Tokyo
Day 13 - Tokyo to Kyoto
Day 16 - Kyoto to Narita Airport

I have looked on HyperDia and priced each train ride individually. The total I arrived at was ¥50,880 or $451. I can see that a nation wide rail pass for two weeks would cost me $400 but since the travel is more than 14 days I'm sort of stumped. Not to mention that I am also not sure the pass would be valid for all of these trips what with the confusing train lines under different systems. Can someone please explain what the wisest course of action is? Thank you so much!


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