when should I activate the pass?

We will be in Japan from the 4th to the 14th of April with the last 4 days in Tokyo.
On the 4th we'll travel from Narita to Shinjuku station area for one night.
On the 5th we go to Fujiyoshida for one night.
On the 6th we head to Kyoto for 4 nights and will using that as our base to visit Hiroshima, Osaka and Nara.
On the 10th we return to Tokyo for 4 nights.
I was thinking it would be most efficient to activate the pass on the 6th for our trip to Kyoto, but this will leave us with days unused at the end. Can we use the pass on the bus from Shinjuku to Fujiyoshida? If so, we should probably start it on the 5th, correct?
Thank you for the help!