So, I reached 55 eggs on my own, and between getting extremely frustrated with the swordfish spike puzzle and a few other things, I decided to just look up a guide.
And hoo boy, am I glad I did. It's true I could have stumbled onto most of these eggs, but to my knowledge there is no tool or technique that could possibly have led me to the correct area, it would have involved wildly increasing numbers of hours just scouring every corner of every room. These were not eggs that were revealed by missing pixels in the map.
Moreover, many of my unsolved mysteries were either actually nothing, unbeatable unless you start a new game, or in Layer 3 (which, having seen some of it, isn't really a thing a person can do on their own).
My recommendation to everyone is to discover every secret you can, exhaust all reasonable avenues of things that look interesting to you, and then crack open a guide. Finding all the eggs without one is possible, but in my opinion, it's going to cross well over into the realm of not-very-fun.
Ultimately, though, a pretty great game. Some great items, unique interactions, and the general vibe of the game sold it for me. Well done to Billy and everyone who helped him!
