My guess is that you would find several scattered references to deafness
in Twain's later writings (especially those not published in his
lifetime), when he rails against God for burdening us with dire
ailments.

One example would be the episode starting in Chapter VII of The
Mysterious Stranger.  Satan changes Nikolaus's fate to give him an early
death by drowning:  "If I had not done this, Nikolaus would save Lisa,
then he would catch cold from his drenching; one of your race's
fantastic and desolating scarlet fevers would follow, with pathetic
after-effects; for forty-six years he would lie in his bed a paralytic
log, deaf, dumb, blind, and praying night and day for the blessed relief
of death..."  Taken from the traditional version (p. 698  of The
Portable Mark Twain).  Your student might also try the Berkeley edition
of Mysterious Stranger manuscripts.

I'm too lazy to find this, but isn't some of that outrage likely based
on Clemens's memories of a Hannibal boy who went deaf very young?  The
name "Tom Nash" sticks in memory, but might be wrong.  Somewhere in the
autobiographical writings (or a letter?) Clemens describes a late visit
to Hannibal where this now old man came up to him in front of a crowd,
glanced at his fellow citizens, and more or less shouted, "Same damn
fools, Sam!"

Anyway, I suspect you'll find bitter references to deafness sprinkled
through those later writings that focus on Twain's quarrels with God.

Mark Coburn