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: 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 - E231-500 - https://www.1999.co.jp/eng/10298502
Ginza Metro Line - Shibuya - Asakusa - Tokyo Metro 01 Series - Ginza Line EMU - https://www.1999.co.jp/eng/10064866
Narita Express - Narita - Ofuna via Yokohama/Hachioji via Shinjuku - E259 series Narita Express - https://www.1999.co.jp/eng/10309650
Ueno-Tokyo Line - Tokyo - Ito - E233-3000 series - https://www.1999.co.jp/eng/10204403
Odawara Line - Tokyo - Odawara - Odakyu 50000 series (Romancecar) - https://www.1999.co.jp/eng/10457066
Tokaido Rapid Line - Hamamatsu - Ōgaki - 313-0 series - https://www.1999.co.jp/eng/10298507
Nara Line - Kyoto - Nara - 205 series - https://www.1999.co.jp/eng/10048721
Tohoku Shinkansen - Tokyo - Shin-Aomori - E5 Hayabusa & E6 Komachi - https://www.1999.co.jp/eng/10271473
Tokaido Shinkansen - Tokyo - Shin-Osaka - 300 Series - https://www.1999.co.jp/eng/10048672
Sanyo Shinkansen - Shin-Osaka - Hakata - 500 Series - https://www.1999.co.jp/eng/10164260
Kyushu Shinkansen - Hakata - Kagoshima - N700 series - 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
I hope this is visible, as station names are tiny due to the scale.
Bigger scale: 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 - E231-500 - https://www.1999.co.jp/eng/10298502
Ginza Metro Line - Shibuya - Asakusa - Tokyo Metro 01 Series - Ginza Line EMU - https://www.1999.co.jp/eng/10064866
Narita Express - Narita - Ofuna via Yokohama/Hachioji via Shinjuku - E259 series Narita Express - https://www.1999.co.jp/eng/10309650
Ueno-Tokyo Line - Tokyo - Ito - E233-3000 series - https://www.1999.co.jp/eng/10204403
Odawara Line - Tokyo - Odawara - Odakyu 50000 series (Romancecar) - https://www.1999.co.jp/eng/10457066
Tokaido Rapid Line - Hamamatsu - Ōgaki - 313-0 series - https://www.1999.co.jp/eng/10298507
Nara Line - Kyoto - Nara - 205 series - https://www.1999.co.jp/eng/10048721
Tohoku Shinkansen - Tokyo - Shin-Aomori - E5 Hayabusa & E6 Komachi - https://www.1999.co.jp/eng/10271473
Tokaido Shinkansen - Tokyo - Shin-Osaka - 300 Series - https://www.1999.co.jp/eng/10048672
Sanyo Shinkansen - Shin-Osaka - Hakata - 500 Series - https://www.1999.co.jp/eng/10164260
Kyushu Shinkansen - Hakata - Kagoshima - N700 series - 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