Thank you, Jib71.
I said transportaion in Japan is not cheap because we are budgeting our trip for 2 people. We estimate it will be about: 12,440 yen (2 people RT to Narita), 10,000 yen (Hakone Free pass for 2 people), 56,600 yen (2 people 7-day JR Passes) = 79,040 yen not including local transports in Osaka, Tokyo, Kyoto.
But we understand that we won't regret this trip.

"If you were to move your Ghibli museum day to the front of your trip, you might fit your Tokyo to Kyoto return trip and the trip to NRT within seven days."
Just need to clarify here - We plan to "activate" our JR Pass as day 1 on June 22 to go to Kyoto. So I can only use JR pass to Ghibli Museum either on June 28 'right?

Sorry - still trying to figure out the math.