I agree with Paul. What you are trying to do is asking for frustration and not going to be pretty. Here are some resources:

• How to create a table of contents in Microsoft Word by Shauna Kelly
• Generating a Table of Contents - Complex Documents

Long term, you are going to have the most easily-edited Word document if you copy text from the converted PDF file into a new document as plain text and then do your formatting in that document using styles, including the Heading styles.