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The term alignment refers to the logical progression of ideas between the structural elements of the dissertation.
This guide is simple to understand and follow.
When your Chair and committee members talk about achieving alignment, they are referring to the logical progression from the introduction, to the problem statement, to the purpose statement, to the research questions and hypotheses (if you have a quantitative study), and to the methodology, and all of this has to align with your theoretical framework, and logically lead into your assumptions, delimitations, and limitations.
As an academic editors, lack of alignment between and among elements in the dissertation is the single biggest problem I see. Lack of alignment can delay your progress.