tokyo->kyoto->osaka-NRT

Hi! This will be the first time me and my sister will be traveling to Japan alone, and the Japanese Rail and subway systems are a bit overwhelming. I have been trying to google up guides and solutions but still have some unanswered questions. Please help recommend cheaper routes or ways of travel based on our itinerary. Any help is very much appreciated.The trip is set in May, not directly after the Golden Week.

Day 1 Arrival at Narita at 3pm, head to tokyo
Day 2 Northern Tokyo area(Skytree, planning on booking an accomodation near Skytree)
Day 3 Western Tokyo area(Shibuya and Shinjuku)
Day 4 Central Tokyo area
Day 5 DisneySea
Day 6 Depart for Kyoto (planning on activating 7 day JR pass here), quick trip to Arashiyama
Day 7 Fushimi Inari
Day 8 Depart for Osaka
Day 9 USJ
Day 10 Osaka kaiyukan aquarium, Dotonbori at night
Day 11 Osaka castle, Osaka Museum and various shrines
Day 12 Umeda Sky building, Abeno Haruka, etc
Day 13 Depart for Narita Airport from Osaka, flight is at 5pm

Would it be better to get a 14 day JR pass or utilize the 7 day JR pass? Also would it be beneficial to obtain a SUICA or Pasmo card to travel around Tokyo for the first few days or is the JR pass going to cover some of the places I will be visiting in Tokyo, Kyoto and also Osaka? Or would it be better to buy metro passes to cover the first few days of traveling in Tokyo and use the Suica for the remaining travels that are not covered by the JR pass?

Also have a few questions regarding the Suica card, I haven't been able to see how much you have to top up the card if you're traveling to places back & forth, for example, head to Central or Western Tokyo from Northern Tokyo, since I am planning on booking an apartment there. Would it be wise to travel back and forth so much? I have booked a place in Kyoto wherein the travel would be covered by the JR pass. As for Osaka, I have not really planned the itinerary specifically because I'm still very much confused and overwhelmed by how I should travel around Tokyo.