Need help with what passes work best in each region

Hey, I'm planning to go to Japan and already have hotels covered for 2 weeks. But now am confused about what passes are worth it (i.e. am I supposed to get JR 7 days, 14 days, or not at all) and what passes to buy where. My itinerary is roughly as follows:

Tokyo:

1. NRT airport to Ebisu station
2. Ebisu station to Shibuya station
3. Ebisu station to Ginza station
4. Ebisu station to Asakusa station
5. Ebisu station to Shinjuku station

Mount Fuji, Kyoto, Osaka:

1. Ebisu station to Fujisan station
2. Fujisan station to Kyoto station
3. Kyoto station to Inari station
4. Kyoto station to Torokko Arashiyama station
5. Kyoto station to Universal City station

Tokyo:

1. Universal City station to Daiba station
2. Daiba station to NRT airport

Sorry if it seems like too much, but if someone could provide any advice (even if it's for a particular region, that would be awesome). Thanks in advance