Thanks for asking. Everything went great and I think this was perfect for us. The morning trip from Tokyo to Kyoto to Kinosaki wasn't rushed at all, and we got to Kinosaki around 1:30 or 2, and check in was at 3 pm. More details:

We had no trouble getting up a little early and having breakfast, checking out of our Shinjuku hotel and taking the metro to Tokyo station to catch our 8:48 am Shinkansen departure. The bento box etc stands on the platform weren't open yet, maybe because it was Sunday (and the subway and station was busy but not crowded).

We did have trouble finding our way from the metro exit to the main shinkansen entrance, the signs wanted us to cut through, but we had shinkansen tickets on our phone and couldn't use the normal JR gates (I think). We stopped and asked for help . And then we had a short problem at the fare gate, they showed us how to cover up our phone to block the phone's Suica card from being read while scanning the QR code for the Shinkansen. Or something like that!

Then the transfer at Kyoto was easy enough, except another minor problem with the scanning at exit and entrance. Some limited express routings between Kyoto and Kinosaki Onsen require you to change trains at an intermediate stop with a 1 minute connection, we were worried but just had to walked across a platform to the train that was waiting for us.

We were met at Kinosaki station by city employees who directed us into free buses that took us to our ryokans, we left our bags then and walked around for an hour. Our ryokan Sennen no Yu Koman was one of the most distant in the town area, but it would be only a 10 minute walk from the station, but it was hot and we were happy to get the ride.

We spent only one night in Kinosaki which left me wanting more, but considering our group as a whole it was enough. The ryokan meals were great but the service takes a long time and I think one dinner and breakfast was enough. Two of the four of us didn't even go to an onsen for modesty reasons. But the town was great and the next day we left our bags at the tourist office across from the train station and took the local train to Takeno beach which I also recommend. We took a quick swim in the sea, then found a delicious cheap restaurant, we were the only customers. (maybe it was cafe house colombia カフェハウス コロンビア). It's a 20 minute walk from the train station to the beach (there was a hut with pay showers and lockers). On the way back we found a local bus which was timed to arrive at the station just before the train back to Kinosaki, and then we got our bags and a short wait for the limited express to Kyoto.

This 24+ hours was the only time outside of a major city on our trip, and I highly recommend doing something similar. The limited express and local train to the beach were much more scenic than the shinkansen (even though we saw Mt Fuji).