Before I start I am going to say that you must complete the entire level for the secrets to fully stick and save to your game, I confirmed this myself. And don't skip any of the ones that you think you already got, even if you know you have them, just go back and be thorough, the easiest way to get messed up on big tasks like this is to think you already did something, let me tell you, it isn't fun having to do it all over again.
After a wee bit of a wait you guys finally are able to figure out how to get all those durned secret areas. And this is a whopping 48 minute video too, so get comfy, we gon' be doing this for a while.
I would suggest opening up the video in youtube to read the description, but I will say this much here, a secret area is found when you hear a metallic sound, you'll know it when you hear it. When you find an area, MANUALLY save the game right away, some times you have to interact with an item first for the secret area to count, do what the video says to the letter.
Prologue: 0
Chapter 1: 0
Chapter 2: 7
Chapter 3: 5
Chapter 4: 4
Chapter 5: 5
Chapter 6: 5
Chapter 7: 4
Chapter 8: 2
The City: 41
Big thanks to PowerPyx for taking the time to upload the video.