Here's a better overview of the layout superimposed over a map of Japan. Obviously, the Tokyo area is enlarged to allow for some nice routes there, but I'm happy with the way it fits.
I hope this is visible, as station names are tiny due to the scale.

Bigger scale:Â https://i.imgur.com/hRnSSE2.jpg
Train lines and trains I will be using - using real trains that still are or have been servicing those lines:
Yamanote Line - full circular route -Â E231-500 -Â https://www.1999.co.jp/eng/10298502
Ginza Metro Line - Shibuya - Asakusa - [font=Roboto, Arial, sans-serif]Tokyo Metro 01 Series - Ginza Line EMU -Â https://www.1999.co.jp/eng/10064866[/font]
Narita Express - Narita - Ofuna via Yokohama/Hachioji via Shinjuku -Â [font=Roboto, Arial, sans-serif]E259 series Narita Express -Â https://www.1999.co.jp/eng/10309650[/font]
Ueno-Tokyo Line - Tokyo - Ito -Â [font=Roboto, Arial, sans-serif]E233-3000 series -Â Â https://www.1999.co.jp/eng/10204403[/font]
[font=Roboto, Arial, sans-serif]Odawara Line - Tokyo - Odawara -Â [font=Roboto, Arial, sans-serif]Odakyu 50000 series (Romancecar) -Â https://www.1999.co.jp/eng/10457066[/font][/font]
[font=Roboto, Arial, sans-serif][font=Roboto, Arial, sans-serif]Tokaido Rapid Line - Hamamatsu - [font=sans-serif]Ōgaki - 313-0 series - https://www.1999.co.jp/eng/10298507[/font][/font][/font]
[font=Roboto, Arial, sans-serif][font=Roboto, Arial, sans-serif][font=sans-serif]Nara Line [/font][/font][/font]- Kyoto - Nara -Â 205 series -Â https://www.1999.co.jp/eng/10048721
Tohoku Shinkansen - Tokyo - Shin-Aomori - E5 Hayabusa & E6 Komachi -Â https://www.1999.co.jp/eng/10271473
Tokaido Shinkansen - Tokyo - Shin-Osaka - 300 Series -Â https://www.1999.co.jp/eng/10048672
Sanyo Shinkansen - Shin-Osaka - Hakata -Â 500 Series -Â https://www.1999.co.jp/eng/10164260
Kyushu Shinkansen - Hakata - Kagoshima - N700 series -Â https://www.1999.co.jp/eng/10871342
I think this is a complete list now. Not sure I can/want add to the complexity, but of course any feedback and corrections are welcome 🙂