i'll just have a full day in Tochigi.Tochigi??
Now as u say it'll need additional 1-2 hrs, it seems not doable within time availability (need to go to Yokohama at least around 5 pm).
For the round trip, you will need an additional 4 hours.
Do you have any idea how to arrange the route so that we can go to the shrine? Or shall I delete other place?
You could take the ropeway up Mount Komagatake where Motomiya is located. But note that access to the lower station of the ropeway is not straight forward if you are using the Hakone Free Pass. I think it might not be worth the effort.