1 Apr - Arrive at Narita Airport and spend the night in Tokyo.
2-4 Apr - Tokyo with sidetrips
Spend three full days in Tokyo with one day spent on a daytrip to nearby Nikko. Also consider one of our suggested Tokyo itineraries.
5 Apr - Tokyo to Kyoto
In the morning, travel by shinkansen from Tokyo to Kyoto (3 hours). Spend the afternoon and evening exploring Kyoto.
6-8 Apr - Kyoto with sidetrips
Spend three full days in Kyoto. Consider one of our suggested Kyoto itineraries. Take a daytrip to nearby Nara and a half day trip to Himeji to check out Himeji Castle.
9 Apr - Kyoto to Tokyo
In the morning, take the shinkansen from Kyoto to Tokyo (3 hours) and spend the afternoon and evening in Tokyo.
10 Apr - Depart from Narita Airport
Depart Japan from Narita Airport.
This is the sample itinerary that I will most probably be following.
I'll spend 2 Apr to catch the cherry blossom at Tokyo.
Slight deviation from the itinerary would be, I am thinking of heading to Kyoto on the 3rd and come back to Tokyo on 7th morning. Thereafter, I'll fly back on 10th.
So it'll be 1 full day Tokyo, 5 days Kyoto (3 full days + 2 days commuting Tokyo - Kyoto), 2 full days Tokyo
The reason to come back on the 7th was to check out Harajuku on Sunday. But I am not sure whether it is worth it or not.
Jr pass is used mainly to cover the longer, more expensive trips on shinkansen and limited express trains. Whether it is worth it to get the pass depends on where u are going.
Will be easier to advise if u post ur itinerary here.