PDF not faithful to source document

Using Create PDF Online I can no longer exactly replicate the source MS/Word document as a pdf. Every conversion option including the default 'Screen' results in a readable (OCR) document that paginates differently from the original. No good for legal documents that (1) must be copied accurately and (2) have internal page references that are no longer accurate.

Thanks for your feedback. Unfortunately, I have more questions:
I have the Standard version of Acobat and do not see Document > Restore in my menu options. Is there another path for Adobe Acrobat Standard?
I am delivering this PDF to customers. I need the PDF to launch from the Web, and open to page 1. If I set the document properties, using Document > Restore, will the settings apply to the PDF that the customer downloads? Or, will the setting only work on my computer?
The first three pages of the PDF are set to Roman numerals (i, ii, iii) and then continues to Arabic numerals (1, 2, 3). Does setting page 1 to a Roman numeral affect how the PDF opens?
Thank you for your help!

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