Clothing advice for November trip to Hiroshima, Kyoto and Tokyo

I'm traveling to Hiroshima -> Kyoto -> Tokyo from November 2 – November 12. How warm should my clothes be at that time of the year?

Will a Patagonia Nano Puff jacket with a t-shirt under it be enough?

Also, should I bring more breathable shoes or is it going to be too cold in November, and should I bring something more like leather sneakers or even boots? My feet typically run very warm.

Thank you!