If Doc Scratch was ectobiologised from Lil Cal, then how did the souls of Caliborn, Gam (yes, I'm calling half of Gamzee 'Gam) and ARquiusprite were transferred from Lil Cal to Doc Scratch? Does ectobiology also take and duplicate the component of an object/individual?

It was a manifestation by proxy, it’d seem like Caliborn can project his Soul through the Lil Cal doll, and in turn, through something made from the Lil Call Doll, such as Doc Scratch.