In _Mark Twain's Notebooks & Journals, vol. 1_, (Univ. of California
Press, 1975) Clemens writes:
"Hanging the negro in the Chinchas" (p. 253)
"Capt Wakeman & the nigger hung" (p. 336)
In the reference notes to _Roughing It_ (Univ. of California Press,
1993) the editors suggest that Clemens "reversed the roles of the
Negro and the white bully" (p. 677).
It seems likely the story in the _Chicago Republican_ is the correct
version. And also that Clemens's awareness of racial issues prevented
him from using a true version of the story in _Roughing It_.
As an aside note --
Edgar Wakeman was also member of the San Francisco Vigilance Committee
which made headlines in 1851 for lynching a prisoner. The news reports
from San Francisco that I have found do not indicate the race of the
man who was hung -- only that he was a convict from Sydney.
I have found no news reports of the lynching in the Chinchas.