OP, go where you want, please be sure to check the price of your train trips to the price of your JR pass. If it is within 5000 JPY I would just buy the tickets as I needed them ( my opinion ). Nikko is nice, and depending on the time of year can be exquisite ! Hakone can be "done" as a day trip from Tokyo, depending on the weather/season your chances of seeing Fuji will vary! Nara is interesting because of the things to see, it is also worth the time. Choices !!!