JR Pass for Tokyo-Kyoto-Hakone rout

Hello!

I'm looking for the validation to the idea that I can use JR Pass for travelling from Tokyo to Kyoto to Hakone/Mt.Fuji and back to Tokyo.
I do know that it doesn't apply to Nozomi trains, so will there be enough Hikari trains in all those directions?

Another question: do all these destinations belong to Tokaido Shinkansen? If yes, is it possible to buy some pass for this line only, for cheaper?

Is it realistic to assume about 3hr rides for all three parts of the rout?

Regarding seat reservations, is it too late to make them 2 or 3 days in advance?

Thank you

I'm looking for the validation to the idea that I can use JR Pass for travelling from Tokyo to Kyoto to Hakone/Mt.Fuji and back to Tokyo.

Yes, except transportation inside the Hakone/Mt.Fuji region.

I do know that it doesn't apply to Nozomi trains, so will there be enough Hikari trains in all those directions?

Yes, two trains per hour in both direction.

do all these destinations belong to Tokaido Shinkansen?

Tokyo and Kyoto yes. Hakone and Mount Fuji are a short bus or train ride from Mishima, Atami and Odawara Stations along the Tokaido Shinkansen.

If yes, is it possible to buy some pass for this line only, for cheaper?

No.

Is it realistic to assume about 3hr rides for all three parts of the rout?

No. The ride from Hakone to Tokyo is considerably shorter. You can check the transportation pages of each destination for details:
http://www.japan-guide.com/e/e623a.html

Regarding seat reservations, is it too late to make them 2 or 3 days in advance?

During most times of the year, no.

Very helpful.