Heya, sorry for the super late reply.
So, I did what you've said - Redid all endings for all 3 girls, gone through all Grace dates and hidden Marion scenes. And I still can't get past 99%.
I also still can't trigger the Nightmare Secret either. I've restarted the game multiple times and didn't see it, despite having every ending unlocked.
As for why I took so long to answer - I started playing on Android, and moved my save file over to PC, and when I couldn't get to 100%, I figured it maybe could be something related to changing platforms, so I decided to wait for the Android release to get 1.02 to see if would allow me to 100% the game... guess that wasn't the case.