I like the update, the flower count on each level was a smart addition, as with the hints, though they are worded a bit strangely. And I like the additions to the Layer 3 level.
Speaking of which, I've encountered a bug that's preventing from me progressing in that level. In the 2D part of it after pressing the button, I go to the weird thing and activate it and after that it just took me to a black screen? I think it's supposed to load a new level but it's just complete darkness for some reason, and if you walk around in the dark level long enough it just takes you back to the eyeball platformer room from earlier.
Also, this could be a fault on my part but I cannot for the life of me find this computer town the hint talked about. Does the mall level have two flowers instead of one? Because it says I'm missing one despite grabbing the one in the dark floating city level you get through via the mall level.
Btw you should clarify you can hammer jump on the floating eyeballs in the new level, because when I died them I think "Oh, i should stay away from those" and then spend the next 10 minutes trying to make an impossible jump.
Other than that, the changes made were pretty good, would love to see what you'll make next.