So I guess the problem and possibly the solution lies with the converter program. I don't know the one you mention, but OmniPage Pro which includes a PDF to Word function allows you to retain (or not) headers and footers.
It would be worth checking in options or setup in the program for header and footer options.
I would expect that if the PDF to Word program, as it finds a new header it will start a new section, so that it can save the new header &/or footer.
If this is the case, I wrote a short routine which takes the header in each section and places it before the first paragraph in that section and takes the footer and places it after the last paragraph in the section.
I have only tried it on a small document and have no idea how it might work in a complex converted document. Some PDF to Word documents make extensive use of frames to hold and position text, and I don't know how this macro would work.
You are welcome to try this macro - it would be placed in a new Module in the Normal document in the VB window (Alt + f11).
If you try this, make sure that you work with backup copies of your documents as the changes cannot be undone with the Undo button.
Note that this is a very basic macro with minimal testing!
Dim objSect As Section
Dim rngHdFt As Range
For Each objSect In ActiveDocument.Sections()
Set rngHdFt = objSect.Headers(1).Range
Set rngHdFt = objSect.Footers(1).Range
objSect.Range.Paragraphs(objSect.Range.Paragraphs.Count - 1) _