Converting from PDF adds massive complexity to an otherwise simple document and this is responsible for most of your problems. The Word converter has made good guesses at how to display the page numbers with fields and 'start at' numbers but ultimately, you are blazing a trail that doesn't make logical sense for fields to be involved in.

IF it was me doing this task, I would be converting the Big Book from PDF and stripping out ALL the section breaks and extraneous formatting. I would change the page setup and styles to ensure that everything that fitted a page in the original PDF still fits on a page or less. Then I would add a Paragraph at the start of the page which includes the header info (ie the PDF page number) - I wouldn't put this into the header unless I was sure that I was not going to expand the content beyond what a page can hold. Finally, I would start adding the 'red text' by using the Comment feature in Word. This would then appear in a sidebar of the page and be the physical equivalent of writing in the margins of the big book.

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Andrew Lockton
Chrysalis Design, Melbourne Australia