5 days itinerary Sept 26-30 - Tokyo with day trip to Mt. Fuji and Kyoto or Osaka

Hi there,

We're planning to get the 7 days JR pass with only 5 days itinerary from Sept 26 to 30, 2014.
Would like to know if should get a JR pass or just buy the normal tickets for 5 days?

Here are our itineraries:
Day 1 (Sept 26 - Fri) - Narita Airport to Shinjuku, Tokyo - where our hotel is.. booked for 5 days already :d
Tout around the city (Shinjuku, Shibuya and Ginza)

Day 2 (Sept 27 - Sat) - Tokyo city tour (Shinjuku Gyoen National Garden, Meiji Shrine, Tokyo Imperial Palace, Tokyo Tower, National Museum, etc.) Any suggestions?

Day 3 (Sept 28 - Sun) - Mt. Fuji and Hakone day tour

Day 4 (Sept 29 - Mon) - Kyoto or Osaka day tour or maybe an overnight stay
Which do you suggest, Osaka or Kyoto? How long is it from Tokyo? Is this covered by the JR pass?
We can stay here overnight and then return the next day to Tokyo.

I know Kyoto has lots of temples to visit to. Are they open on Mondays? With Osaka, what else is there to visit aside from Universal Studios?

Day 5 (Sept 30 - Tues)
Option 1 9am from Osaka or Kyoto back to Tokyo (stay in Tokyo til 2pm)
Then Tokyo to Narita Airport (our flight is at 650pm)

Option 2 Osaka direct to Narita Airport (how long is the travel time?)
Our flight is at 650pm, we should be at the Narita airport before 4pm.

Looking forward to your response. Your suggestions will be much appreciated.

Thanks in advance!