The difficulty for me with that one was essentially due to the fact that I climbed the "inverted well" before getting the eye powerup, so I was sure all of them were dead ends. Indeed, to actually notice the new passageway one actually needs to follow the correct path, not simply get to the screen, because it is pretty much invisible and the detector only fires when we are very close... I am not sure how I would fix that, though. Changing the architecture would of course be too much, but perhaps extending the detector signal a bit farther away, so that one can see it even when going up the big path?

You enter it from above. Look for a secret passage on the right wall of that pit, one screen above the bottom, if I am not mistaken.

You enter it from below. You have to use the green powerup a couple of screens below.

Once you reach that screen on the right you should be able to figure out what to do with these.