Hi there!
Here's a quick run down of the best routes to take.
Tokyo - Kyoto, directly by Shinkansen from Tokyo to Kyoto station. ¥ 13,800 / 158 Minutes
Kyoto - Gotemba Shinkansen from Kyoto to Atami station, local trains from there to Gotemba. ¥ 12,900 / 197 Minutes
Gotemba - Tokyo local train to Mishima, from there Shinkansen to Tokyo ¥ 5,040 / 102 Minutes.
For a total of ¥ 31,740 in travel costs. The 7 day JR pass is ¥ 29,110 so you are currently looking at ¥ 2,630 in savings. Remember that the JR Pass is also good for local travel around Tokyo and Kyoto on local JR lines and you could also use it from travel to and from the airport, adding more to your savings.
Hope this helps!
Daniel