I've always thought it of it as God imputes a soul to a frontal lobe if it can support it in lieu of grave variables (I mean, this would explain why the mentally ill still have souls). So far I don't have any proof that God *hasn't* imputed a soul into a frontal lobe.
There was this kid who didn't have a brain and only a brainstem:
I'd have to argue there that there is no soul in that instance since... a soul can't run on a *brain stem*.
I suppose cloning isn't so much the question as genetic engineering. What specific sequences of DNA are required to the point where soul imputation is invalid? Obviously the brain has a system (and seizures are neural chaos), but because one can operate with half a brain and severe brain damage... it's hard to say.
Of course genetic engineering can eradicate corrupt traits, like sickle cell anemia or colour blindness (and technically blue eyes are a corruption as well-- since the melanin deployment is prematurely halted on the iris: which is why most albino humans have blue eyes as well). I think that would be great to be honest, but modifying human genetics poses a lot of problems so I don't think society will ever accept it. People are difficult enough to convince that GMO foods are okay (I am fine with GMO foods).
*on the topic of eye colour, probably the best compromise is green and then amber being next (both of which are less common
than blue and dark brown). The two 'extremes': dark brown allows better day vision, but blue allows better night vision (not for contrast but for seeing things in the dark with low levels of light).
Sidenote: I may be a bit biased since my eyes are neither blue nor dark brown, but I've noticed blue eyed folks have trouble seeing in the sun, and dark brown eyed folks can't see very well in the dark.