LaTeX class files (plus barebones working example) of a LaTeX thesis document for a University of Wisconsin--Madison PhD dissertation.
This is what you should add to your document as \documentclass[12pt]{thesis}.
This is the Natbib style file for the BibTeX bibliography (\bibliographystyle{thesis}).
AASTeX addons for thesis.cls, to make sure all the niceties you're used to from emulateapj are still around.