Q:

Do physical disabilities carry over into the Matrix? (And vice versa)

So, I'm writing this fanfiction for the Matrix and my main character is physically disabled. More specifically, her physical pod body was born blind. 
Would she then be blind in the Matrix, or would she have sight because of the whole jack/port in the skull thing?
And what about the reverse? Could someone have like a lost limb from being in say, a car accident in the Matrix, and then when they're unplugged their physical body is perfectly fine?

A:

The avatars, for a lack of a better word, in the Matrix, are mental self-projections of the person. Notice Neo, once removed from the Matrix for the first time, is hairless, pale, scrawny, has atrophied muscles and is completely sensitive to normal room lighting because his muscles and eyes have never been used. In real life, a 20+ year coma would require months of physical therapy to get back to moving around, unlike Neo who only needed a few days/weeks based on how the movie progresses. His vocal chords, sense of smell, even lungs would have been weak (depending on how the pods actually keep the humans viable).
But once he got jacked into the training simulation, and later, the Matrix, as Morpheus explains:

"Your appearance now is what we call residual self-image. It is the mental projection of your digital self."
  ―Morpheus to Neo

The avatar conforms to how the user wants to look, or believes they should look. Digital muscles, clothing, hair cuts, etc. Morpheus is physically stronger than Neo, and has had full use of his physical body for years, while Neo is weak from muscle atrophy.

Morpheus: How did I beat you?
  Neo: You’re too fast.
  Morpheus: Do you believe that my being stronger or faster has anything to do with my muscles in this place? You think that's air you're breathing now? *A Beat* Hah. Again.
  -Training Simulation Scene

Yet after Neo stops thinking of physical limitations in the Matrix, he's as fast and as strong as Morpheus. There are limits to what they can look like imposed by the Matrix of course, basic humanoid, but as everything else in the Matrix, those rules can be bent and sometimes broken.
In real life, physical ability to do something is mutually exclusive to a person's mental self. Phantom limb sensation and phantom pain are common in people who have lost any limb or part of the body. The CNS and PNS still think the limb is there.
But the Matrix does have limitations, which might be a technological limitation OR imposed to maintain order. If a person dies in the Matrix, they die in real life.
It’s speculation on my part, but I think physical trauma in the Matrix can cause Conversion Disorders like paralysis in the real world, the inability to move your muscles but only due to a mental block. It would be treated through typical therapy. The same would apply to physical trauma in the real world being part of the Residual Self Image in the Matrix. The user would have to work around their mental belief of disability just like Neo worked around his belief that he couldn't jump across buildings.

