Request for help with Itenerary

Hello!

We purchased the JR Pass, but are having trouble to determine what routes are available to use it on as well as what trains we need reservations for. We would greatly appreciate help to check and advise on the following itinerary:

1) Narita Airport to Toranomon Hills (-->Andaz Hotel)
2) Toranomon Hills to Kyoto (-->Hyatt Regency Kyoto)
3) Kyoto to Arashiyama
4) Kyoto to Tofuku-ji Station
2) Kyoto to Odawara
3) Odawara to Shimbashi (-->Conrad Hotel)
4) Shimbashi to Harajuku (--> Meji Jingu Shrine)
5) Shimbashi to Shinjuku (-->Park Hyatt)
6) Shinjuku to Tama Center (-->Sanrio Puroland)
7) Shinjuku to Narita Airport

Also, we will have two small suitcases and a small stroller with a toddler. Can you help advise us best times to travel so we may avoid rush hour and whether luggage/strollers can be taken on trains?

Thanks kindly for any help you can offer!