Awesome matchup. However, I have no idea what party Twain was or favored, and he seems to have mainly been on the left--civil rights, anti-imperialism, favoring unions--and whatnot. It'd be fun to see what type of support he could pick up, geographically, given his background. I'd guess the National Democrats do a bit better as well.
In his autobiography, Twain indicates that he was generally a Republican in his middle age, and one of those 19th Century Radical Republicans to some extent, especially as he grew older. There are only three people in his autobiography whom Twain paints a positive picture of- his deceased wife, his deceased daughter, and General Grant, whom he revered. All others are mercilessly skewered.
He did vote for Cleveland in 1884, joining the Mugwumps in their dissatisfaction with James G. Blaine, which caused some social discomfort for himself and the town preacher in their heavily Republican town (voting was public in 1884 Connecticut). I would be surprised (though I haven't researched) if he voted for William J. Bryan in 1896, but I wouldn't be surprised if he voted for him in 1900. He bitterly skewered Theodore Roosevelt as a war-monger, personally arrogant and rude, and deeply unpleasant, so he may well have abandoned his Republican inclinations late in life
