Well, you could always buy a copy of Adobe Acrobat, which is actually designed solely for the purpose of creating and editing PDF files.
Or you could import the file into Calibre, convert it to ePub format, edit the ePub to add the table of contents, then convert it back to PDF.
There are other free tools for working with PDF directly. If you do a Google ...
I will extend on @Donald's answer but I would also like to note I do not recommend, personally for quality issues, ever using Calibre for ebook development.
As stated I would suggest getting a copy of Acrobat and you can (for this example I am using Acrobat X Standard but note the I have not seen any difference in the shortcut buttons BUT the GUI has ...
There are also free tools that allow editing/adding bookmarks. A cross platform example is jPdf Tweak.
It is a little clumsy to use, but you can create the table of contents in your favourite spreadsheet program, export as csv and then just import it.
The short answer is no. The only way to make notes easier to read is to find a book that has been properly formatted to have hyperlinked inline notes. If a book doesn't have that, then you could either request it from the publisher or fix it yourself.
k2pdfopt (free, open source) can also do this by supplying a text file. See the -toclist option. Use like so:
k2pdfopt -mode copy -n -toclist my_chapter_list.txt srcfile.pdf -o outfile.pdf
...where my_chapter_list.txt is a simple ASCII file with page numbers beginning each line, e.g.
2 Table of Contents
5 Chapter 1
25 Chapter 2
I am used to a simple and free tool that adds clickable bookmarks to PDF or DjVU files: http://handyoutlinerfo.sourceforge.net/.
You first have to prepare (and import in the tool) bookmarks entered in a text file as an indented list of labels and pages. Then the tool creates them in the document as bookmarks you can open/reduce and click on using the left ...
Jpdfbookmark can work for scanned books
Prepare the TOC in .txt file
Chapter 1. The Beginning/23
Para 1.1 Child of The Beginning/25,FitWidth,96
Para 1.1.1 Child of Child of The Beginning/26,FitHeight,43
Chapter 2. The Continue/30,TopLeft,120,42
Para 2.1 Child of The Beginning/32,FitPage
You can OCR the TOC and use regex to fix it.