You are following up on a fish market breakfast with Kura Sushi?

Regarding your Day 1 option 1, it seems like you plan on running from place to place like a madman. If you only assign 2 hours to the national museum, why bother? Either you are interested in its content which would make it at least a half-day activity, or you aren't and therefore should drop it entirely. Your option 2 looks a lot better as a first day in Japan if you ask me. It's weird to me that you would assign as much time to walk around Senso-ji as to an entire museum. Similarly on your Kyoto day, 3 hours to explore Gion. Gion is not that big and unless you are booked to go into a place there, "exploring" is basically just walking down Hanamikoji. Sanneizaka is 100x more interesting to explore if you ask me.