There is no magic bullet to cleaning up converted files. The bottom line is that PDF is not intended to be edited. It is a medium for viewing. Essentially an equivalent of a printed copy.

If the original was created from a Word document, and is not protected, then simply opening the PDF in Word might produce a better start point.

As the process that creates the PDF appears to be in house, it would be better to explore whether that process can output to a Word document instead.

You may be able to create a macro that performs the necessary replace functions. e.g. http://www.gmayor.com/document_batch_processes.htm has an option to loist replacements pairs in a table and will run all those pairs on a document, but it will still take a deal of effort to work out what needs changing.

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Graham Mayor - MS MVP (Word) (2002-2019)
Visit my web site for more programming tips and ready made processes www.gmayor.com