Okay, still think you should take my advice above: make a set of linked boxes at the bottom of your page (footnote area). Copy the footnotes as a block (see above), then shift-enter at end of each to force next one into next box. This is assuming that you do want footnotes at bottom of appropriate page. You may have to shift-enter more than once to force some footnotes along a couple of boxes to make them line up on same page as the citation, or shift-enter only after the set of citations for that page.
Regular text is in linked boxes above (regular page area) so be sure to pour that in first, so you'll know where it goes. Start at the front and move to the back, so that if footnotes need extra space, the copy and footnotes are both "squeegeed" back
One thing that might make formatting easier is if the Word formatting is all by added bold and added italic (instead of specific named bold and italic variants). That way they will import into your footnote style, and you can do a find/replace font thingy at the end. If your writer has already changed to "true fonts" instead of "styled fonts", there's not a lot you can do that way.
Sorry, there's no magic bullet on this, only ways to reduce the grunt work. "If it was easy, everybody would do it... and they'd be the competition..."