I just did something similar so maybe I have something to add:
I'd expected to take the first train of the day from Tokyo to Kyoto (around 5am) 9/27 and a very late train back from Kyoto to Tokyo on 9/28. Turns out the first Hikari to Kyoto leaves much later than I expected, and the latest Hikari back to Tokyo is much earlier than expected. Plan was to have the overnight be two full days in Kyoto.
The earliest Shinkansen- Hikari leaves at 6:32am, so you can get to Kyoto by 9:14am. I do no know if there are earlier Nozomi's but the Shinkansen start running at a certain time only.
We recently left Tokyo last week on a 2:30pm Kodama and arrived at Odawara at 3pm, after consulting with the tourist office the ropeway closed at 5pm, all we could do in Hakone was take the Odakyu Railway/Hakone Tozan Train which took 1 hour up to Kowakidani then 30 mins by the H1 (red) bus to Moto-Hakone. This is by the Lake Achi and we arrived at 4:30pm just as the last ferry had left and so we could not take that on its round trip either. We stayed for about 2 hours, by walking along the old Toikado lined with ancient Cedar trees, then hiking around the park and then to the Hakone Checkpoint. By 5:30pm every shop was closed.
We finished by taking the 6:40 H1 bus from Hakone-machi-ko to Odawara which took 1 hour then ran to the Shinkansen for the 7:52 Kodama to Tokyo. (Those guys at the ticket office can issue tickets in a blaze). Arrived at Tokyo Station at around 8:30
6 hours spent, about 3 hours of sightseeing. It was worth it but I would definitely go before lunch next time.
I did 2 nights in Kyoto but only 1 was for sightseeing, the 3rd day was traveling back to the airport. You really have to get up early and stick to a few sights. We did Fushimi Inari before lunch but it took us 3 hours to hike up and down. Then we went to Arashiyama on the other side and that took a couple hours also and everything closed up. Couldnt even squeeze in a visit to Kiyomizu-dera.
The main take away is Google Maps can tell you how long it takes to reach a place but nothing will tell you how long it takes to fully experience a certain location. Kyoto looks small on a map but those blocks are big compared to the blocks in Tokyo, and a lot hotter for some reason.
I totally get what you are trying to do, I managed to squeeze in a lot in 7 days but you are going to be exhausted walking all day from 6am to 10pm and repeat the next day. You could literally spend 7 days in Akihabara and not be done if that's your thing.
Imho stick with Tokyo, enjoy it and Disneyland/Sea. (Btw get to DisneySea at 7am so you can run for the fastpass to Toy Story, its the only line that matters.)
You are not going to have fun on doing 1 night in Kyoto, if you want, make that 1 night in Hakone and you can do your Hakone loop stuff and be fulfilled there.
The JR Pass can be refunded if you dont claim it, just return to where you bought it. It only becomes worth it if you take the Shinkansen more than once like to Odawara and Kyoto, or go to Nara maybe (dont squeeze that in)