What a neat little gem of a game!  There's a bit of grindiness, but at its current size and pacing that didn't bother me, and the rest of it comes together quite solidly.  The previous fixes such as specifying hold-to-gather were definite improvements, and while it does still bottleneck at a few points on mid-game resources (mushrooms mostly), I rarely found myself without some option to progress, not to mention that every run increased power whether I had any crafting upgrades available or not.  Your little helper buddy is a cool mechanic, too (though would often give me new resources from unlocked areas before I was able to properly collect any). 

My only suggestion is to possibly add four more lore notes to the game, and reorder them so that the four new ones become the four in the endgame rooms -- this would put the "missing" notes you've got all game at the end of the list, and wouldn't spoil quite so hard that there *are* endgame rooms until it's time to find them.  (I actually located one halfway through the game, specifically because the missing notes made me start looking for hidden content.)  As a bonus, the new lore notes might let you talk a little bit about the Rainbubble.  That said, this is just about perfect as-is, and thanks for making it.