you must not read much serious literature (sorry if this sounds passive-aggressive, its not meant to be lol)...some pretty famous books that make prominent use of traditionally academic devices like footnotes:

http://en.wikipedia.org/wiki/Infinite_Jest

http://en.wikipedia.org/wiki/House_of_Leaves

http://en.wikipedia.org/wiki/Pale_Fire

house of leaves in particular does a lot of tricks with formatting, including stuff similar to what I'm trying to get to work. my thinking being that if he got it to work there must be some way i can, right?