Well, you can of course try to get FM generate the PDFs as you need and append them as needed.
Or you decide to extend your FMP with a big toolbox, e.g. MBS Plugins.
With MBS Plugin and the DynaPDF add-on, you can import PDF, add page numbers, add new pages with text, place links to jump between pages or to websites and save a new PDF.
Maybe download and play with examples?
After you print the first PDF, you can save the last page number in a global variable or global field:
Enter Preview Mode
Go to Record/Request/Page [Last]
Set Variable [$$lastPageNumber ; Get ( PageNumber )]
Then, you'll need a calculated "pageNumber" field to place on any additional layouts you want to add:
$$lastPageNumber + Get ( PageNumber )
Use preview mode to see the numbering.
Just speaking to the "Table of Contents" part of your question. The table of contents usually appears at the front of a book, and an index usually appears at the back — if either exists at all. I just want to put in a plug for my favorite word processor, Nisus Writer Pro (unfortunately Mac only), which provides useful tools for automating those features directly from the text you're working on:
It is possible to create a TOC in FileMaker by using a script to preview each section, go to the last page and capture the page number. (Page number + 1 is the page number of the following section.)