Tokyo: follow the Shinkansen line name
Tokyo Station serves several high-speed corridors. Tokaido and Sanyo services towards Kyoto and Osaka use a different area from many JR East services towards northern Japan and Hokuriku. Start from the exact train on your ticket, then follow the relevant signs. Marunouchi and Yaesu are opposite sides of a large complex.
Shinagawa can be convenient, but it is a different stop
Shinagawa can be practical for south Tokyo and some Haneda connections on the Tokaido corridor. It does not substitute for Tokyo on every product or every line. Choose your departure station deliberately and do not assume you can board elsewhere simply because the train passes through it.
Kyoto: check the exit for your hotel
The Hachijo side is convenient for many Shinkansen entrances; the north side faces Kyoto Tower and the principal city bus area. Local JR, subway and Kintetsu connections are separate services. Use your destination address to select an exit and avoid walking through the whole station with luggage twice.
Shin-Osaka: include the city transfer
Shin-Osaka serves high-speed trains. Osaka Station, Umeda and Namba are other locations connected by conventional rail and subway. Look at the total hotel-to-platform journey when comparing departure times. Do not select Osaka Station when you mean the Shinkansen station.
A realistic station routine
For a first visit, arrive about 30 minutes before departure and add more time for ticket collection, unfamiliar transfers or heavy bags. Check the departure display again after entering the gate. Platforms can change; a guide cannot replace the live station display. Locate your car marker and queue without blocking the walking route.