Hm. I'm still a bit confused, but I'll work it out. I took another Shira route in the meantime and boy, I had no idea what I was getting yself into T_T.
Acting upon the feedback I've received, I decided to add a "Clue Chart" to the newest build of the game. It will show you which clues you managed to find (and which you didn't) in a character's route the moment you trigger a single bad ending for that character. You will find this chart in the Quick Menu of the game (right in-between the "Load" and "Settings" buttons). Once you get stuck, the chart should give you some kind of idea what routes to explore in order to advance further. I hope this little addition will help you out!