We need to use the Japan Rail Pass from Tokyo airport (NRT) to Mount FUJI and later to Kiso

Hi there,

You can find the details here for Narita Airport:
https://www.jrpass.com/blog/getting-from-narita-airport-into-tokyo-with-and-without-the-japan-rail-pass

For Fuji:
https://www.jrpass.com/blog/itinerary-tip-mt-fuji

and for Kiso:
It depends on where you are coming from, likely you'd take a train to Nagoya station and transfer there to a train bound for the Kiso valley.

Hope you find this useful,
Daniel