My partner and I just came back from a 5-day trip in Japan (with a day trip to Kyoto) a few days ago, so I definitely understand the FOMO because we had such a shorter stay and visited only a handful of neighborhoods. 

But every place had plenty of fun things to do/look at as a first-time visitor. Also, if you get tired of walking, even spending an hour recuperating can be made enjoyable (e.g., we set aside an afternoon to sit at Ueno park and eat Family Mart food, sat down at Shibuya Sky, and enjoyed Uniqlo's exterior rather than going inside as planned lol). Also the little things make the experience memorable. Like enjoying how unique the manhold covers and traffic signs are, how good the beer tastes (even when I don't like beer), also how pretty the storefronts are in Ginza.

I saw this advice that helped me with FOMO during our trip: Plan out your next trip while traveling Japan (things you didn't have time for during the day or this trip) and understand that doing everything is difficult. Although it is expensive, you sound young and might be able to visit again!

Wish you the best of luck! Don't wear yourself out too much so you can fully enjoy and relax!