1.
The shape of the characters visualizes tightness and pressure. The form is a translation of the phonology and the corresponding letter feeling.
2.
The silences show the activity of speaking, even if you don't hear anything. Besides, they they emphasize the length of time.
3.
Stotts is an interactive script: letters change contextually, depending on the sound combination. This because the same letter does not always produce the same stutter.
For example, an R behind the K can soften the sound, while a vowel makes the K very sharp. Also, the last letter of a word is always fluent, even if this is a difficult letter. That's why the alphabet of Stotts contains different characters for the same letter.