Thank you @technocrat. The intermediate tex file created by the Rmarkdown file is in the example. This tex file fails to compile due to the hypertarget call, but will compile if I replace \hypertarget{title-of-my-first-chapter}{% \chapter{Title of my first chapter}\label{title-of-my-first-chapter}} with simply \chapter{Title of my first chapter}. That's why I was thinking it may be beneficial to remove the autoidentifiers all together using the pandoc_args option in bookdown::pdf_book. Included below is the tex file I'm using as a template that is being filling in with the markdown content and YAML fields.
\documentclass[boldheadings,thrmdefs,bbm,ams]{USFDissertation}
%% Set basic information about the disseration
\title{$title$}
\author{$author$}
\degree{$degree$}
\department{$department$}
\college{$college$}
\university{}
\majorprofessor{$majorprofessor$}{Ph.D.}
\committeemember{$committee1$}{Ph.D.}
\committeemember{$committee2$}{Ph.D.}
\committeemember{$committee3$}{Ph.D}
\committeemember{$committee4$}{Ph.D}
\keywords{$keyword1$}{$keyword2$}{$keyword3$}{$keyword4$}{$keyword5$}
\approvaldate{$approvaldate$}
\copyrightdate{$copyrightdate$}
%% Begin the document itself
\begin{document}
%% Make a title page
\maketitle
%% Maybe dedicate it to someone
\begin{dedication}
$dedication$
\end{dedication}
%% Acknowlege your intellectual debts
\begin{acknowledgment}
$acknowledgment$
\end{acknowledgment}
%% Insert a table of contents
\tableofcontents
%% Insert a table of tables -- comes before figures in the format.
\listoftables
%% Insert a table of figures
\listoffigures
%% Include an abstract
\begin{abstract}
$abstract$
\end{abstract}
%% begin the body of the dissertation
\dissertation
$body$
%% End of dissertation
\end{document}
I adapted this from the original template tex file which is this:
\documentclass[boldheadings,thrmdefs,bbm,ams]{USFDissertation}
%% Set basic information about the disseration
\title{Dissertation Title}
\author{Doctoral Candidate Name}
\degree{Doctorate of Philosopy}
\department{Mathematics \& Statistics}
\college{Arts and Sciences}
\university{}
\majorprofessor{Advisor Name}{Ph.D.}
\committeemember{Committee One Name}{Ph.D.}
\committeemember{Committee Two Name}{Ph.D.}
\committeemember{Committee Three Name}{Ph.D}
\chair{Committee Chair Name}{Ph.D}
\keywords{KeyWordOne}{Key Word Two}{KeyWord Three}{Key WordFour}{KeyWordFive}
\approvaldate{Month Day, Year}
\copyrightdate{Year}
%% Include whatever macros you like
%% Some people like these:
% \def\beq{\begin{equation}}
% \def\eeq{\end{equation}}
%% Begin the document itself
\begin{document}
%% Make a title page
\maketitle
%% Maybe dedicate it to someone
\begin{dedication}
Tx xxx xxxxx xxx xxxxxx xx xxxxxxxxxx xxxx xxx Fxxxxxxx Dxxxx Txxxxxx xxxxxxx xxxx xx xxx xxxxx xx xxxxxxx xxxxxxx.
\end{dedication}
%% Acknowlege your intellectual debts
\begin{acknowledgment}
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxx xx X. Xxxxxxxx, xxxxx xxxx xxx xx xxxxxxx
xxxxxxxxx, xxx.
\end{acknowledgment}
%% Insert a table of contents
\tableofcontents
%% Insert a table of tables -- comes before figures in the format.
\listoftables
%% Insert a table of figures
\listoffigures
%% Include an abstract
\begin{abstract}
Lxxx xx xxxxxx xxxxxx'x xxxxxx xxx xxx xx xx xxxxxxxxxxx xx xxxx xx
\[x_{x=1}^{xxxxx}x{1}{x^x}=x(x)=0,\]
xxxx $R(x) = x{1}{2}$.
Txxx I xxxx xxxxx xxxx xx xxxxxx xxxx-xxxxxx xxxxxxx xxxxx xx xxxx
xxxx xxxx xxx xxxxxxx xxxx xxxx x xxxxx xxxx xx Exxxx'x.
\end{abstract}
%% begin the body of the dissertation
\dissertation
%% Chapter One:
\chapter{First Chapter Name}
Txxx I xxxx xxxxx xxxx xx xxxxxx xxxx-xxxxxx xxxxxxx xxxxx xx xxxx
%% Chapter One, Section One:
\section{First Section Name}
Txxx I xxxx xxxxx xxxx xx xxxxxx xxxx-xxxxxx xxxxxxx xxxxx xx xxxx
%% Chapter One, Section One, Subsection One:
\subsection{First Subsection Name}
Txxx I xxxx xxxxx xxxx xx xxxxxx xxxx-xxxxxx xxxxxxx xxxxx xx xxxx
%% Chapter One, Section One, Subsection One, Subsubsection One:
\subsubsection{First Subsubsection Name}
Txxx I xxxx xxxxx xxxx xx xxxxxx xxxx-xxxxxx xxxxxxx xxxxx xx xxxx.
%% Reference to table
See Table \ref{table:1} on page \pageref{table:1}
%% Citation
\cite{PXX}.
%% Figure One:
\begin{figure}
% \begin{center}
% \includegraphics{}{}
% \end{center}
\caption{First Figure Caption}
\end{figure}
%% Chapter Two
\chapter{Second Chapter Name}
%% Table One:
\begin{table}[h!]
\begin{center}
\begin{tabular}{c|c|c}
First Column&Second Column&Third Column\\
Second Row& etc. & etc.\\
Third Row & etc. & etc.
\end{tabular}
\end{center}
\label{table:1}
\caption{First Table Caption}
\end{table}
%% Figure Two:
\begin{figure}
\caption{Second Figure Caption}
\end{figure}
%% Chapter Three:
\chapter{Third Chapter Name}
%% Chapter Three, Section One:
\section{First subsection in chapter three.}
%% Theorem and proof -- using theorem-like environments from thrmdefs
\begin{theorem}
Ix $R(x)>0$, xxxx $x(x)=0$ xxxxxxx \[R_x=x{1}{2}.\]
\end{theorem}
\begin{proof}
Ix $R_x x>0$, xxxx $\sin(x)=0$ xxxxxxx \[R_x=\frac{1}{2}.\]
\end{proof}
%% Table Two:
\begin{table}[h!]
\begin{center}
\begin{tabular}{c|c|c}
First Column&Second Column&Third Column\\
Second Row& etc. & etc.\\
Third Row & etc. & etc.
\end{tabular}
\end{center}
\label{table:2}
\caption{Second Table Caption, xxxxxxxxx xxx xxxxxxxx xxxx xxxxxxxxxxx xxxx xxxxxxxx \hspace*{.25in} xx xxxxxxx}
\end{table}
%% Table Three:
\begin{table}[h!]
\begin{center}
\begin{tabular}{c|c|c}
First Column&Second Column&Third Column\\
Second Row& etc. & etc.\\
Third Row & etc. & etc.
\end{tabular}
\end{center}
\label{table:3}
\caption{Third Table Caption}
\end{table}
%% Reference section
\begin{thebibliography}{99}
\bibitem{PXX}X. X. Xxxxxxx. ``Xxxxx xxx xxx xx xxxx.'' \emph{Xxx Xxxxx}, \textbf{123}, 4567
\end{thebibliography}
%% About the author
\begin{bio}
Bxxx xx xxx xxxxx xx Txxxxxxx, I. Txxx Yxxxx xxxx xxxx xx xxxxx
xxx xxxx xxx xxx xxxxxxxx xx xxxxx xxx Rxxxxxx xxxxxxxxxx. Sxx
xxxxxxxx xxxxxxx xx xxxxxxx xxxxxx, xxx xx xxxx xxxxxxxxxxxx
xxx xxxxx xxxxx xxxx xxxx-xxxxxx xxxxxxx. Dxx xx xxx xxxx xxxxxx
xxxxxxxx, xxx xxxxxxxxx xxxx xx xxxxxxxxxxxxxxxx xxxxxxxxxxxx,
xx xxxx xx-xxx xxxx xxxxx xxxxxx xx xxx xxxxxx xxx xxxxxxxxx
xx xxx xxxxx xxxxx.
\end{bio}
%% End of dissertation
\end{document}
