I was just there recently and there are rooms off to the side of the David which had so many sculptures. I remember it vividly because they all had these black markings sticking out of them in symmetrical places all over the faces and bodies. Is this what you're speaking of? I can't remember seeing the works in progress, as you mention.
I thought it was at that museum, perhaps it was another. The statues were clearly incomplete. The arms and legs were often still just a block of stone, uncarved. I'll dig through my photos later to see if it was a different location.