We just did this trip - returned last month. It is fabulous. I'd had a tip from Joyce on this Forum to buy a small 5X7 blank journal sold at all shrines. There is usually someone/monk who will "sign " with calligraphy and stamps. The mark for each shrine is unique and beautiful, and is a neat souvenir. I'm going to frame mine. We did a day trip to Nara (Triple Lights Mr. Kzauo was our guide from Kyoto) and loved that a lot. Hired Tours by Locals Mr OIgawa-san when we arrived in Tokyo to help us navigate and he was great. There is not a lot of dedicated time for shopping, not that it is my primary focus, but just a hint to be alert for things wherever you go. Imperial Gardens should be great in the fall in Tokyo, and/or the bamboo forest area.
Arriving a day early (9/13) for Essence of Japan and would love to meet fellow travelers for touring and/or dinner.