This is an excellent question. The CMOS does cover the punctuation used to properly write a stutter.

Hyphens and Dashes 6.75.

Ellipses and suspension points 6.15, 13.48 - 56

Capitals 7.48

Capitalization 2.63, 8.1 - 2, 5.5, 5.6

But first, before we can determine where the stutter is to be placed, we have to understand how people stutter. Most stutters occur on the first phoneme of a word. There are 42 phonemes in the English laguage. You can find the list here: http://www.auburn.edu/academic/education/reading_genie/spellings.html

An example would be:"ph-ph-phoneme" or "p-p-pet" or "d-d-David"

(yes, notice the capitalization of 'David', regardless of use, stutter or otherwise, names are capitalized)

Once you know where to break the word for the stutter, then it is time to decide which of the stutters to use.

To break a thought in a sentence use the ellipses:

"I just... I just can't do it anymore."

To have a long pause stutter use the em-dash: (You will have to pretend I'm using an em-dash, Markdown doesn't format well. To make an em-dash in word, ctrl-alt-minus sign

"I ju--ju--just can't do it anymore."

To have a staccato stutter use the en-dash.

"D-d-d-David, st-st-stop!"

But, in most stutters, and the most widely accepted for, just use the hyphen:

"I th-th-think I un--understand now."

However, once you know the rules, you can use artistic license to break them, just remain consistent throughout the text.

R.L. Wolf, Writers Coordinator

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Wolfenshire, Moderator/Community Leader