Since I have no idea what your 'main overhaul macro' is, I can't comment on that. Regardless, what you want is as simple as:
Code:
Sub ReFormatFtNts()
Application.ScreenUpdating = False
Dim FtNt As Footnote
With ActiveDocument.Range
For Each FtNt In .Footnotes
With FtNt.Range
.Font.Reset
.InsertBefore "[["
.InsertAfter "]]"
End With
Next
End With
Application.ScreenUpdating = False
End Sub