Actually, it is acceptably straightforward to include a custom header in org-mode. Basically you can create your own latex class in customize-group org-export-l

Actually, it is acceptably straightforward to include a custom header in org-mode. Basically you can create your own latex class in customize-group org-export-latex and then add a #+LATEX-HEADER: \input{stuff.tex} to your file to include the appropriate header magick. I'm currently using this approach to prepare my thesis in org-mode.