OK, if you are willing to bite the bullet on this, my recommendation would be to copy it all into Word as plain text. Use the pdfs as references on how you want it to look.

Keep in mind that the pdf text may be the result of an OCR process. If it is, there will be errors in the typing as well as the other problems that come from converted documents.

Start with a Word template with numbering based on Styles following the directions on Shauna Kelly's page: How to create numbered headings or outline numbering in Word 2007 and Word 2010. This may take some time to set up the first time but it will be time well spent.

Use Styles for all of your formatting. That way, when you want to change how [an indented quotation] looks, you can change the look in one place and have it apply to everything.

Read Tips for Understanding Styles in Word
How styles in Microsoft Word cascade
How to create a table of contents in Microsoft Word
Understanding Styles in Microsoft Word

Skimming these is OK, you want to be familiar with the ideas and concepts, though. A couple of hours skimming these up front may save you weeks of work later.