For adding the parentheses to Word's formatted footnote references, I'd suggest a wildcard Find/Replace, where:
Find = *
with the Find Style specified as 'Footnote Reference'; and
Replace=(^&)
That will add the parentheses to the footnote references in both the body of the document and at the start of the footnotes also. You can then make all of these non-superscript by changing the 'Footnote Reference' Style.

If you want to limit the action to just the body of the document, don't modify the Style; instead, before doing the Find/Replace, create a new Style based on the 'Footnote Reference' Style named, say, 'Footnote Reference (Body)' without the superscript format, include the new Style's name as one of the Replace parameters, then select the whole of the document body (Ctrl-A). When you execute the Find/Replace and Word asks whether you want to continue, answer No.

__________________
Cheers,
Paul Edstein
[Fmr MS MVP - Word]