It looks like we have at least one part of the answer - that the character will appear in the film. The Hollywood Reporter has the news that Dennis Haysbert of 24 is in talks to replace Duncan in the role for next year's Sin City: A Dame to Kill For.
The film has already begun its shooting schedule but is reportedly on and off throughout December and then will begin shooting full time in January, meaning that it's likely Haysbert is in no particular hurry to hammer out the terms of his deal; he can always join the shoot in 2013.
That said, there doesn't appear to be any doubt on the part of the filmmakers that they've got a deal in principle and Haysbert will be appearing in the sequel.
"Manute is a character that has been part of the heart of the Sin City tales, and the late Michael Clarke Duncan beautifully established that role onscreen," said co-directors Robert Rodriguez and Frank Miller in a statement to THR. "We could not tell the story of Sin City: A Dame to Kill For without Manute and are thrilled to welcome Dennis Haysbert to the cast."
Haysbert most recently appeared alongside Spider-Man's own Tobey Maguire in The Details, a comedy with Elizabeth Banks that was just released via video on demand channels. He can be seen in the theaters in Wreck-It Ralph.