
Congratulations on your litter; sorry about the little one that got overlaid. Does the whelping box have pig rails?
Personally I'd have the little one with the cleft put to sleep; the surgery that it'll need when it's older can be very risky, and if they survive they never thrive. As the palate is the roof of the mouth I'm not sure how a cleft palate can be outside the mouth? It's not really consistent to say "If I hadn't fed the little one is most probably would have died by now so I feel that I've done the right thing by feeding it. " and then say that you wouldn't want to pts but would rather nature took its course! You're stopping nature doing just that ..
She probably has diarrhoea, especially if it's black, from eating the afterbirths and should be shortlived. She'll need easily digested food for a while until her insides get back to their normal positions after being squished by a belly full of puppies! Also the discharge from her vulva could last for several weeks - as long as it's not profuse or smelly this is normal, just as with human mothers. The placental sites on the uterus wall bleed and the blood has to escape!
She's probably snapping at you because she's trying to guard her babies and keep them together. It sounds as though she's getting anxious with the little one being taken away from her so often, and wants it to stop.