Day 1 Narita to Tokyo Day 2 Tokyo Day 3 Tokyo to Nagano Day 4 Nagano to Kyoto Day 5 Kyoto to Osaka day trip, back to Kyoto Day 6 Kyoto to Tokyo Day 7 Tokyo to Narita
Not a difficult question at all. Why not get a 7 day JR Pass? Your itinerary makes it worth it. You can activate it at Narita Airport and use it on the Narita Express into Tokyo, then to all the cities you list. Within Tokyo you can also use it on the Yamanote Line, which goes to many popular tourist areas. Might not be enough for every place within Tokyo you'd want to visit, but it can still be helpful.
As a suggestion, since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg and Abeno Harukas Bldg are wonderful. Instead, for your Day 5, I suggest you visit Nara, which has several must-see places, especially within Nara Park.
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As a suggestion, since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg and Abeno Harukas Bldg are wonderful. Instead, for your Day 5, I suggest you visit Nara, which has several must-see places, especially within Nara Park.