If your journey only include
a) roundtrip transfer to NRT
b) a day or two of local travel in Tokyo
c) roundtrip bullet train between Tokyo and Kyoto
d) day or two of local travel in Kyoto
Then
please do check out vendor mentioned in post 15 above.

For some reason, "experts" on Japan forum very rarely or never mention it.
Few years back, I stumbled upon it and turn out to be both much cheaper and more convenient than Japan Pass (It allows use of Nozomi trains which are not only faster but more importantly runs every 10 minutes - no reservations or preplanning necessaey except during very peak perioids)

For NRT traansfer and local Tokyo travel I use NEX and SUICA which I just noticed are much cheaper in USD terms now due to FX rate changes.