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After you've arranged your PDF file the way you want it, if you'd like to add a Table of Contents, there's several possible ways to do this. Two are:
Create the Table of Contents page or pages in MS Word, install it into Acrobat, and then use Acrobat's tools to create the links between Table entries and the actual pages of content.
Create a set of pages in an MS Word file that are section headings or starters. Then, use MS Word's Table of Contents feature to auto-build the Table of Contents, which are links to each of the section pages. Add this file to your PDF file. Lastly, move the section pages to their appropriate places in the document, so that the Table of Contents created in Word helps readers navigate to the different parts of your PDF file. This second option is best when you need to compose opening remarks for each section of your file.