PhD dissertation different from master thesis; What might I be able to do about methodology?
If you are accepted into a PhD program, you should consider your dissertation topic to be independent of, and separate from your masters thesis topic. A PhD dissertation is fundamentally different from a Masters thesis.  A PhD dissertation is expected to make a new contribution to research (however small), whereas a Masters thesis is a summary and application of existing research.  PhD dissertations are a deeper dive into a topic or research questions, and an attempt to shed new light on the topic or questions.

You may have a Masters thesis that leads naturally into a deeper investigation as a PhD dissertation.  Or not. You should focus your attention on the topics and questions that motivate your interest in a PhD.  What are the core, unanswered questions?  Which of these questions can you, with your skills and interests, address with some chance of success?  

Leave behind the details of your Masters thesis.  Focus on what you have learned in the process, and what new skills or capabilities you have.  Now, with these insights, you should engage with surveys of research in your field -- those describing the unsolved problems or most critical questions.  How does your experience, education, and interests lead you to engage with these unsolved problems or critical questions?