I have tried my best to reduce my code to a MWE. I have a thesis document which has separate files. To show the problem I have removed all the text and just included 1 chapter in this MWE. The main file is as below:

\documentclass[12pt]{report}
\renewcommand{\familydefault}{\rmdefault}

\usepackage{harvard}
\usepackage{amssymb}
\usepackage{amsmath}

% TAMU Thesis Packages
\usepackage[latin9]{inputenc}
\usepackage[letterpaper]{geometry}
\geometry{verbose,tmargin=1.25in,bmargin=1.25in,lmargin=1.4in,rmargin=1.15in}
\pagestyle{plain}
\usepackage[doublespacing]{setspace}
\usepackage{tocloft}
\usepackage[rm, tiny,center, compact]{titlesec}
\usepackage{indentfirst}
\usepackage{epstopdf}
\usepackage{graphicx,float,wrapfig}
\usepackage{etoolbox}
\usepackage{tocvsec2}
\usepackage[titletoc]{appendix}
\usepackage{appendix}
\usepackage{tamuconfig}
\usepackage[font=singlespacing]{caption}

\include{defs}

\begin{document}
\renewcommand{\tamumanuscripttitle}{An analysis of bubble plumes in unstratified stagnant water}
\renewcommand{\tamupapertype}{Dissertation}
\renewcommand{\tamufullname}{Chung Kei Chris LAI}
\renewcommand{\tamudegree}{Doctor of Philosophy}
\renewcommand{\tamuchairone}{Scott A. Socolofsky}

\renewcommand{\tamumemberone}{Kuang-An Chang}
\newcommand{\tamumembertwo}{Hamn-Ching Chen}
\renewcommand{\tamudepartment}{Civil Engineering}

\input{../lists}

\pagestyle{plain}
\pagenumbering{arabic}
\setcounter{page}{1}

\input{../ch_01}

\end{document}


The list file is as follows:

\phantomsection

\begin{singlespace}

\setlength{\cftaftertoctitleskip}{1em}
\renewcommand{\cftaftertoctitle}{%
\hfill{\normalfont {Page}\par}}

\setlength{\cftbeforechapskip}{0.2cm}
\setlength{\cftbeforesecskip}{-0.4cm}
\setlength{\cftbeforesubsecskip}{-0.45cm}

\tableofcontents

\end{singlespace}

\pagebreak{}

\phantomsection

\renewcommand{\cftloftitlefont}{\center\normalfont\MakeUppercase}

\setlength{\cftbeforeloftitleskip}{-12pt}
\renewcommand{\cftafterloftitleskip}{12pt}

\renewcommand{\cftafterloftitle}{%
\\[4em]\mbox{}\hspace{4pt}FIGURE\hfill{\normalfont Page}\vskip\baselineskip}

\begingroup

\begin{center}
\begin{singlespace}

\setlength{\cftbeforefigskip}{0.6cm}
\setlength{\cftbeforetabskip}{0.4cm}

\listoffigures

\end{singlespace}
\end{center}

\pagebreak{}

\phantomsection

\renewcommand{\cftlottitlefont}{\center\normalfont\MakeUppercase}

\setlength{\cftbeforelottitleskip}{-12pt}

\renewcommand{\cftafterlottitleskip}{12pt}

\renewcommand{\cftafterlottitle}{%
\\[4em]\mbox{}\hspace{4pt}TABLE\hfill{\normalfont Page}\vskip\baselineskip}

\begin{center}
\begin{singlespace}

\setlength{\cftbeforetabskip}{0.7cm}

\listoftables

\end{singlespace}
\end{center}
\endgroup
\pagebreak{}


Chapter 1 is as below-

\chapter{\uppercase{Budget of turbulent kinetic energy in bubble plumes by acoustic Doppler velocimetry (ADV)}}
\label{ch_TKE}

\begin{flushright}
{\it Everything is theoretically impossible, until it is done.''} - Robert A. Heinlein
\end{flushright}

\section{Introduction}\label{sec:intro}

\section{Laboratory experiments}\label{sec:expt1}

\subsection{Set-up}

\subsection{Some experiences working with the profiling ADV - Vectrino II}    \label{sec:2_3}

\subsection{Doppler noise estimation and noise-reduced estimates of the stress tensor}

\subsection{Decomposition of streamwise velocity w} \label{sec:5_2}

\subsection{Wavelet analysis on streamwise velocity $\tilde{w}$}

\section{Summary and discussions}\label{sec:conclusion}

\pagebreak{}


The tamuconfig file is as follows:

\ProvidesPackage{tamuconfig}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%   Titlepage Commands
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newcommand{\tamumanuscripttitle}{Default Title}
\newcommand{\tamupapertype}{DissertationOrThesis}
\newcommand{\tamufullname}{Full Name}
\newcommand{\tamudegree}{Doctor of Philosophy}
\newcommand{\tamuchairone}{Chair Name}
\newcommand{\tamumemberone}{Committee Member1}

\newcommand{\tamudepartment}{Department Name}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%   Titlesec Customations
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\titleformat{\chapter}{\centering\normalsize}{\thechapter.}{1em}{}
\titleformat{\section}{\centering\normalsize}{\thesection}{1em}{}
\titleformat{\subsection}{\centering\normalsize\it}{\thesubsection}{1em}{}
\titleformat{\subsubsection}{\centering\normalsize\it}{\thesubsubsection}{1em}{}

\setcounter{secnumdepth}{3}

{\protect\cftdotfill{\cftsecdotsep}}}  % puts leader dots on chapters.

%%%%%%%%  Remove the extra vertical space before chapter titles when using     report class %%%%%%%%%%%
\makeatletter
\def\ttl@mkchap@i#1#2#3#4#5#6#7{%
\ttl@assign\@tempskipa#3\relax\beforetitleunit
\vspace{\@tempskipa}%<<<<<< REMOVE THE * AFTER \vspace
\global\@afterindenttrue
\ifcase#5 \global\@afterindentfalse\fi
\ttl@assign\@tempskipb#4\relax\aftertitleunit
\ttl@topmode{\@tempskipb}{%
\ttl@select{#6}{#1}{#2}{#7}}%
\ttl@finmarks  % Outside the box!
\@ifundefined{ttlp@#6}{}{\ttlp@write{#6}}}
\makeatother
%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%  TOC Customations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Aesthetic spacing redefines that look nicer to me than the defaults.
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%  Makes the font in the TOC normal.
\renewcommand\cftsecfont{\normalfont}
\renewcommand\cftsecpagefont{\normalfont}

\renewcommand\cftpartfont{\normalfont}
\renewcommand\cftpartpagefont{\normalfont}

\renewcommand{\cftchapaftersnum}{.} % adds a period after chapter numbers in the toc.

\renewcommand\cftsecafterpnum{\vskip\baselineskip} % These lines allow for long toc titles to be displayed single-spaced within.
\renewcommand\cftsubsecafterpnum{\vskip\baselineskip}
\renewcommand\cftsubsubsecafterpnum{\vskip\baselineskip}
\renewcommand\cftchapafterpnum{\vskip\baselineskip}
\renewcommand\cftpartafterpnum{\vskip\baselineskip}

%%%%%%%%%%%  Makes the appear TOC doublespaced and almost singlespaced for sections.
\setlength\cftparskip{-2pt}
\setlength\cftbeforechapskip{0pt}
\setlength\cftbeforepartskip{0pt}
\setlength\cftbeforesubsecskip{-6pt}
\setlength\cftbeforesubsecskip{-6pt}
\setlength\cftbeforesecskip{-6pt}
%%%%%%%%%%%%%%%%%%%%%

%%%%%  These change spacing in the toc.. Leave for now for tweaking.
%\cftsetindents{chapter}{0in}{.3in}
%\cftsetindents{subsection}{1in}{0in}
%\cftsetindents{subsubsection}{1.5in}{0in}
%\cftsetindents{paragraph}{0.5in}{0.5in}

\preto\figure{%  Removes the extra space added before new chapters
}
\preto\table{%  Removes the extra space added before new chapters
}

\renewcommand{\cftloftitlefont}{\hfill\normalsize\rm\uppercase}
\renewcommand{\cftchappagefont}{\normalsize\rm}  % Makes the chapter page     numbers the default size and font.
\renewcommand{\cftchapfont}{\normalsize\rm}

\let\chaptermarkOLD\chaptermark


I want consistent spacing above and below major headings. Since there is a double space between list of tables and chapter 1 heading, I also want the same spacing between chapter main heading and subheading 1.1. The spacing between subheadings that is 1.1 and 1.2 is fine and doesn't need any changes.

• What is tamuconfig.sty? And please don't use \it ... -- it's outdated. Use \textit{...} or \itshape... – user31729 Dec 10 '15 at 21:31
• tamuconfig.sty is a file in the thesis template. Dont know really know what its for – Shray Sharan Dec 10 '15 at 21:39
• Without it, the code throws an error – Shray Sharan Dec 10 '15 at 21:40
• Well, how should we compile without it? – user31729 Dec 10 '15 at 21:40
• @Johannes_B I think Dan should answer. It isn't my suggestion, after all. – cfr Jul 17 '16 at 18:16

The tocloft package allows the setting of many spaces and dimensions. In this case it seems you want the space above section (and maybe subsection) lines to be larger. The file posted has the line
\setlength{\cftbefo‌​resecskip}{-0.4cm}

If the dimension -0.4cm is changed to something positive, it would cause the space above toc section lines to be larger. I refer you to the documentation of the tocloft package for other possible customizations.