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.