LDS belief in pre-existence of the human person vs. human physical deformities This other question discusses the Mormon doctrine of pre-existence prior to conception.

The highest rated answer quotes from The Encyclopedia of Mormonism that says, on the page "Pre-Existence (Pre-Earthly Existence)" that (emphasis added):


  It is Latter-day Saint doctrine that living things existed as
  individual spirit beings and possessed varying degrees of intelligence
  in an active, conscious spirit state before mortal birth and that the
  spirit continues to live and function in the mortal body. The
  revelations teach that premortal spirit bodies have general
  resemblance to their physical counterparts.


I wanted to ask some questions about the part that the "premortal spirit bodies have general resemblance to their physical counterparts" (to get an understanding of the reasoning behind this):


When it comes to people born with physical deformities (weirdly
shaped limbs, missing body parts, both male and female genitalia,
etc.), are these deformities then also present on that persons
spirit body?
If they are present in their spirit body, why would that be the
case? (i.e. shouldn't the spirit body be created perfect or is there
some reason why it would not be?)
If they are not present on the spirit body, why would they be on the
physical body if there is an expectation of general resemblance
between these two?
As it says in the quotation, "The revelations teach that premortal spirit bodies have general resemblance to their physical counterparts."  The key word there is "general."

The LDS explanation is that such imperfections are tied up with Adam and Eve, and the Fall of Man.


  The man and the woman had now become mortal; through indulgence in food unsuited to their nature and condition and against which they had been specifically warned, and as the inevitable result of their disobeying the divine law and commandment, they became liable to the physical ailments and bodily frailties to which mankind has since been the natural heir. Those bodies, which before the fall had been perfect in form and function, were now subjects for eventual dissolution or death.
  
  James E. Talmage, Jesus The Christ, chapter 3, The Need of a Redeemer.  (Emphasis added)


As a result of the Fall, the conditions of immortality and physical perfection that Adam and Eve enjoyed while in the garden were stripped from mankind, and we became subject to the problems and tribulations of mortal life.  Humanity was cast out of the paradise of Eden into a harsh, hostile environment that would grow "thorns and thistles" and require a great deal of effort to overcome.  And indeed, birth defects are generally caused by some external factor causing something to go wrong with the gestation process.

However, Latter-Day Saints believe that such physical deformities are just that: physical problems, unrelated to our eternal spiritual identity.  In this video clip, the Apostle Dallin H. Oaks speaks of birth defects and other lasting physical deformities, assuring us that they will be corrected in the Resurrection, when our bodies are made immortal and perfected, restored to "their proper and perfect frame."