Hmm, its been so long since I beat the game that I don't remember everything anymore, I just remember that the item in that cave was the only one I had trouble finding, which means that item in lime grotto I found without any problems.
Lime grotto... Did you destroy every stone with M-mode, maybe this item is inside one of them, otherwise I don't know. I still have the game, so if you provide save I can try to take a quick look, I just don't want to start the game from begining.