Thank you for keeping it difficult

[Commando Peach]

The only time I got legit stuck so much I quit the game was...

Spoiler below!

...trying to find the third elevator rod in the study. I had quickly looked away when my vision started blurring because of that window cracking (the one you need to break to get around the rubble), and then didn't give it more than a passing glance later on. It wasn't until I quit and restarted the level later that I saw the cinematic of it cracking and realized it was there. Aughhhhhhhh.

As for the...

Spoiler below!

...trapdoor by Agrippa, I thought I was stuck for a while too. I was convinced the machinery I needed was the machinery in the room on the left side of the Chancel with the unmoving door. Eventually I lapped the whole area, from Nave to Chancel, a few times, using my eyes and not my ears. Eventually I went back to Agrippa in hopes he'd help, and that's when I heard it and investigated.

I'm pretty sure that puzzle is there to remind you sometimes need to listen more than look.