Why did #1.......
have those weird eyes and "Hair Tufts"?
Any symbolism there?
My guess...he's a representation of the "core" of the Scientist's soul so, therefore, looks most like him. Also, in that same vein, #1 was the first stitchpunk doll made so it's not too much of a stretch that the Scientist modeled the look of the doll after himself anyway.
I have learned from experience... that a modicum of snuff can be most efficacious.