Just some feedback on your nomenclature advice; apparently there’s some trouble with what you describe (I don’t know how you got that working, actually); here’s an example that seems to work properly: (also note the convenient \jobname command)

\immediate\write18{makeindex \jobname.nlo -s nomencl.ist -o \jobname.nls}
\documentclass{article}
\usepackage{nomencl}
\makenomenclature
\begin{document}
$x=y$
\nomenclature{$x$}{horizontal}
\nomenclature{$y$}{vertical}
\printnomenclature
\end{document}

Cheers,
Will