Check out the stuff I did with Pod for Mastering Perl. There's a chapter on messing with and extending Pod, and I wrote the book in O'Reilly's PseudoPod format (see Pod::PseudoPod), an extension of Pod that includes footnotes.

The Pod chapter also talks about writing your own Pod translator. It's not as hard as you think. You start with one that's close to what you want and override the parts that you want to change. Look into Pod::Simple.

Good luck :)