If you don't have a JR pass and only need to travel between NRT-Tokyo-Kyoto and back it is not a dire situation if you didn't have a JR pass.

In the end the amount spent just for that route is nothing major if you just spent on regular tickets (it might cost you a bit more but you can even use Nozomis), or getting a discount ticket from Kyoto back to Tokyo. Considering overnight fedex probably costs a pretty penny, the costs would of probably have been offsetted a bit already.

As mentioned once you get to Kyoto station you can use a short taxi or take a short subway ride from Kyoto station to shijo karasuma station (I think the Shijo Karasuma Station is the closest), if you have some luggage I recommend the taxi.

Note the JR Pass is not valid on Subways, trams, monorails, etc etc.