It's worth recalling that, from the viewpoint of the general reader,
Jefferson wrote only one book--his Notes on the State of Virginia.  I should
imagine that any other "works" by him likely to appear in a home library of
Twain's day might be  a few speeches, letters or other papers in collections
of classic American documents.

There may well be Jeffersonian influence in some of Clemens' thoughts on
slavery and especially his thoughts on the tendency of slavery to make a
brute of the master.  Passages about slavery in  Pudd'nhead Wilson, the
Autobiography, and Following the Equator have the same flavor as some of
Jefferson's thoughts in the "Notes."

I apologize for being too lazy to check my quote, but . . . One sentence, in
Puddn'head Wilson (or possibly the Autobiography?) is a virtual paraphrase
of a line in Notes on the State of Virginia:  Twain says (in effect) 'wasn't
it natural for a slave to snitch hams from the smokehouse considering that
the master had stolen his freedom?'  In "Notes," Jefferson says the same
thing in more legalistic language.

To me, these echoes don't necessarily prove that Sam had read Tom.  They
were surely the thoughts of many troubled, intelligent Southerners over the
generations.

If I were seriously interested in possible connections between Jefferson and
Twain, and Twain's possible responses to the place of Jefferson in American
history & myth,  I would focus on Pudd'nhead Wilson:
--For what it shows of the hypocrisies of slavery and what slavery could do
to masters.
--For the treatment of the miscegenation theme in the light of the endless
gossip about Jefferson and "Black Sally," as well as many another Southern
account of miscegenation.  [To digress:  I've often wondered how much
Faulkner had Pudd'nhead Wilson in mind when he wrote, say, the Ike McCaslin
stories.]
--For the harshness or near despair of what Twain seems to be saying about
'the American Dream' vs. American historical realities;  for example, the
barb beneath the joke in that final epigraph:  "It was wonderful to find
America. But it would have been more wonderful to miss it."
--For the satire of the "First Families of Virginia."

Mark Coburn