This is my sort of question, since I have basically the same setup as you do (except I use Vim, not Emacs.)
My novel text looks like this:
% Novel Title
# Title 1
Text goes here.
# Title 2
More text goes here.
This works fine for me, since Pandoc wants to convert the top-level section markers
# into chapter breaks, exactly as intended. The only snag is that there isn't any easy way to indicate scene breaks, so I wound up using a literal
\# to mark scene breaks (since the
# is the scene break marker in standard manuscript format). I pass the author information and other metadata as variables on the command line when I invoke Pandoc.
Depending on how fancy you want your output to look, it may be worthwhile to get your text through an intermediate format such as RTF. The RTF format is human-readable (in theory), and Pandoc lets you create the RTF doc from a template so that you can specify your fonts, headers, etc. Note, however, that getting a good RTF template set up could take you several hours of experimentation.