I asked in the reno thread but gonna paste it here too:
You got any thoughts? What are the chances of 11:45 then manage to clear customs?
I did the 9.35pm flight 2 times already and I usually stay at the airport hotel and take the Haruka in the morning as I was tired after the flight. I arrive in kyoto ard 10 plus, stuff my luggage in the lockers and go sightseeing as my airbnb had a check in time of 3pm.
The other option would be taking the bus and arriving at the Kyoto station at 1am and depend on your hotel or airbnb, you either have to walk somemore or take taxi.
If you don't think you will be tired after the flight, you can do go straight to kyoto. Kansai is not so busy at night. If everything is as per normal, you should be able to clear customs in 45 - 60 mins. The taxi shuttle you linked to, do wait for the last internation flight so I am pretty sure if you provide all your flight information, they can wait for you.