Also i'm searching for the flute as we speak, when i find i'll save and install it 
Don't drive yourself nuts looking for that. A lot of stuff in KF games are in secret passages etc. I know there's equipment in KF2 I've not found before after 3 playthrus throughout my life. Afaik you can finish DD without the flute.
You'll probably miss some stuff even if you go the OCD route of trying to open every square inch of wall. I love the secret wall aspects of KF but were it up to me, I'd probably make finding the mechanisms to open them even harder than just pressing the event button within like a 1m radius (translation spamming the event button while sliding down a wall)
The best secret walls to me are the ones that are kind of intuitive. But the out of the blue ones are fun too.
PS: If you're trying for "100%" if even possible... I believe a number of points come from rare drops.
