Depois de alguns minutos no google, notei que você precisa do seu próprio LaTeX-Template, que pode ser passado como uma opção para o pandoc:
pandoc --toc --chapter --template=yourtemplate.tex -o output.pdf input1.mkd
No entanto, seu modelo precisa de algumas modificações no site do LaTeX. Como sugestão, você pode usar:
Como ponto de partida, você pode usar o seguinte modelo. Eu copiei o modelo padrão link e adicionei algumas coisas extras.
Tenho certeza de que você pode remover a maioria das combinações if-end. O modelo precisa ter mais opções para os usuários.
\documentclass[chapterprefix=false,titlepage=false]{scrreprt}
\usepackage[T1]{fontenc}
\usepackage{amssymb,amsmath}
\usepackage{fixltx2e} % provides \textsubscript
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\usepackage[utf8]{inputenc}
$if(euro)$
\usepackage{eurosym}
$endif$
\else % if luatex or xelatex
\ifxetex
\usepackage{mathspec}
\usepackage{xltxtra,xunicode}
\else
\usepackage{fontspec}
\fi
\defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
\newcommand{\euro}{€}
$if(mainfont)$
\setmainfont{$mainfont$}
$endif$
$if(sansfont)$
\setsansfont{$sansfont$}
$endif$
$if(monofont)$
\setmonofont{$monofont$}
$endif$
$if(mathfont)$
\setmathfont(Digits,Latin,Greek){$mathfont$}
$endif$
\fi
% use microtype if available
\IfFileExists{microtype.sty}{\usepackage{microtype}}{}
$if(geometry)$
\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
$endif$
$if(natbib)$
\usepackage{natbib}
\bibliographystyle{plainnat}
$endif$
$if(biblatex)$
\usepackage{biblatex}
$if(biblio-files)$
\bibliography{$biblio-files$}
$endif$
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
$if(tables)$
\usepackage{longtable}
$endif$
$if(graphics)$
\usepackage{graphicx}
% Redefine \includegraphics so that, unless explicit options are
% given, the image width will not exceed the width of the page.
% Images get their normal width if they fit onto the page, but
% are scaled down if they would overflow the margins.
\makeatletter
\def\ScaleIfNeeded{%
\ifdim\Gin@nat@width>\linewidth
\linewidth
\else
\Gin@nat@width
\fi
}
\makeatother
\let\Oldincludegraphics\includegraphics
{%
\catcode'\@=11\relax%
\gdef\includegraphics{\@ifnextchar[{\Oldincludegraphics}{\Oldincludegraphics[width=\ScaleIfNeeded]}}%
}%
$endif$
\ifxetex
\usepackage[setpagesize=false, % page size defined by xetex
unicode=false, % unicode breaks when used with xetex
xetex]{hyperref}
\else
\usepackage[unicode=true]{hyperref}
\fi
\hypersetup{breaklinks=true,
bookmarks=true,
pdfauthor={$author-meta$},
pdftitle={$title-meta$},
colorlinks=true,
urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
pdfborder={0 0 0}}
\urlstyle{same} % don't use monospace font for urls
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\setlength{\emergencystretch}{3em} % prevent overfull lines
$if(numbersections)$
\setcounter{secnumdepth}{5}
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(verbatim-in-note)$
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(lang)$
\ifxetex
\usepackage{polyglossia}
\setmainlanguage{$mainlang$}
\else
\usepackage[$lang$]{babel}
\fi
$endif$
$for(header-includes)$
$header-includes$
$endfor$
$if(title)$
\title{$title$}
$endif$
\author{$for(author)$$author$$sep$ \and $endfor$}
\date{$date$}
\begin{document}
$if(title)$
\maketitle
$endif$
$for(include-before)$
$include-before$
$endfor$
$if(toc)$
{
\hypersetup{linkcolor=black}
\setcounter{tocdepth}{$toc-depth$}
\begingroup
\let\clearpage\relax
\tableofcontents
\endgroup
}
$endif$
$body$
$if(natbib)$
$if(biblio-files)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$biblio-files$}
$endif$
$endif$
$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
$endif$
$for(include-after)$
$include-after$
$endfor$
\end{document}