Thank you for the guide!
Fightscene: choose the right side. If you reach the next answer go into flowchart and choose the last orange hexagon.
Fightscene: choose the left side
■ 第四話 都庁の秘密 私ルート
Self-question ロボはともかく心の整理を
1) ジョン・ドウの警告
I have no idea what happened here, but this option never came up for me - I was only ever able to choose one or the other, and the follow up self-question session on either side didn't have this option.
I went back to the orange hexagon prior to this branch and chose answer 1 (instead of answer 2, which the guide says) and this option came up after I chose the right side (still no follow-up fight). Maybe it should be changed to "WHEN you reach the next answer"?
Also:
音楽取得率100%
unlocked a bit later than indicated here, during the dialogue choices afterwards (before Ending 57)
イラスト取得率100%
unlocked when I went to the Extras menu and actually loaded the pictures (option 4, under FOAF)