Is the JR pass good value for our itinerary?

Hi,

I will be travelling to Japan next month, my itinerary is:

Sun 4th Feb - land in Haneda, travel to Tokyo for 4 nights
Thu 8th Feb - travel to Atami for 1 night
Fri 9th Feb - travel to Kyoto for 4 nights
Tue 13th Feb - travel to Osaka for 4 nights (day trip to Nara)
Sat 17th Feb - travel to Tokyo for 1 night
Sun 18th Feb - travel to Haneda for flight home.

When I used the JR pass calculator, it doesn't seem to be cost efficient to get the pass as the above fares come to 35,840JPY whereas a 14 day JRpass (which actually doesn't quite cover our full itinerary time-wise) is 46,390JPY.

Have I done my maths right? It seems like quite a big price difference.

My above costing doesn't account for travel within the cities; can the pass be used in cities for local transport i.e. subways, buses etc? Would this then make the pass better value than buying a Suica card on top of this?

Feeling quite confused, so any help you might be able to provide would be gratefully appreciated!

Many thanks