Hey Phillip,
This is why one needs to give the true scope of a problem when asking for help.
If you haven't read this it's worth a couple of minutes of your time.
Tip: How Do I Get The Best Answer in the Shortest Time?
Convert backtick-delimited citations to footnotes (Perl) v1.00.kmmacros (7.1 KB)

This is less than elegant, but it gets the job done.
I've thought of at least one way that will probably work in Keyboard Maestro and another method for Perl that's probably more efficient than what I've already done, but I've spent enough time on the problem already.
-Chris