From what Ive found out in my playthroughs, you need to gather the other endings like normal and bad endings to find the clues.
That's the thing, I've done all possible options I can think of and I'm still missing those two clues
Try building up trust between Mariko and Shira, and then don't show her the book. :) Glad to hear you've enjoyed the game!
Thank you so much! That got me the silver clue but I'm still having trouble with the orange one if I could just get one more hint! :)
(EDIT: Nevermind, I was just getting the hint wrong, haha)
(EDIT2: ...and now I'm stuck on how to get anything but Shirr's Bad Endings A and B. The walkthrough cannot come fast enough)
Stay with Shirr whenever you can during the prologue and then in her route, choose the options in which Mariko is suspicious of her. Oh, and don't drink the potions with her, this one's crucial. Shirr's tricky like that. ;)