Marco's and Shirr's routes are a bit tricky. ;3 Near the end of Shirr's route, try going to the library and then going back upstairs again.
Also, 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!
I'm happy to hear that you're enjoying the game so far! Thank you for the wonderful feedback! I hope you'll enjoy the rest of the routes as well, once you manage to unlock them! :)