Spacing issue between section/subsection/paragraph etc

Question

**Update

This might be a repetitive question, but I do not know to prevent this additional white space from showing up.

Attached is my MWE to show additional white space that I have been unable to get rid of. Specifically, page 11 in between the paragraphs and subsections. I need to specify the strict spacing between all sections/subsections/paragraphs etc.

Here is my MastersDoctoralThesis.cls file:

\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{MastersDoctoralThesis}[12/7/20 MastersDoctoralThesis]
\DeclareOption{11pt}{
    \PassOptionsToClass{\CurrentOption}{article} % book report
}
\ExecuteOptions{11pt}
\ProcessOptions\relax
\LoadClass[11pt,letterpaper]{report}
\setcounter{secnumdepth}{5}
\setcounter{tocdepth}{5}
\RequirePackage[utf8]{inputenc}
\RequirePackage[T1]{fontenc}
\RequirePackage{amssymb}
\let\bvec\mathbf 
\RequirePackage{empheq}
\RequirePackage{amsbsy}
\RequirePackage{mathtools}
\DeclarePairedDelimiterX{\norm}[1]{\lVert}{\rVert}{#1}
\RequirePackage{mathpazo}
\newlength{\UOneInChapterSpace}
\newlength{\UHeadSpace}
\newlength{\UDoubleSpace}
\makeatletter
\RequirePackage{calc}
\setlength{\UOneInChapterSpace}{-40pt + 1in} 
\setlength{\UHeadSpace}{3ex}
\setlength{\UDoubleSpace}{1ex}
\RequirePackage{setspace}
\RequirePackage{etoolbox}
\AtBeginEnvironment{figure}{\addvspace{\UHeadSpace}}
\AtEndEnvironment{figure}{\addvspace{\UHeadSpace}}
\AtBeginEnvironment{table}{\addvspace{\UHeadSpace}}
\AtEndEnvironment{table}{\addvspace{\UHeadSpace}}
\AtBeginEnvironment{equation}{\addvspace{\UHeadSpace}}
\AtEndEnvironment{equation}{\addvspace{\UHeadSpace}}
\AtBeginEnvironment{tabular}{\singlespacing}
\RequirePackage{subfiles}
\RequirePackage{lipsum}
\RequirePackage{longtable} 
\RequirePackage{booktabs}
\newbool{graphicDraft}
\DeclareOption{graphicFinal}{\boolfalse{graphicDraft}}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\baseclass}}
\ProcessOptions\relax
\ifbool{graphicDraft}
    {\RequirePackage[draft]{graphicx}}
    {\RequirePackage[final]{graphicx}}
\RequirePackage{subcaption}
\RequirePackage{animate}
\RequirePackage{pdfpages}
\RequirePackage[font=singlespacing]{caption}
\RequirePackage{todonotes}
\RequirePackage{geometry}
\geometry{
    paper          = letterpaper,
    inner          = 1.25in,
    outer          = 1.25in,
    bindingoffset  = 0in,
    top            = 1in,
    bottom         = 1in,
    %head           = 2in,
    %showframe,
}
\RequirePackage{xcolor} % Required for specifying custom colors
\definecolor{BLACK}{HTML}{000000}
\definecolor{URED}{HTML}{CC0000}
\definecolor{midnightBlue}{HTML}{145680} % midnight blue
\definecolor{darkBrown}{HTML}{654321} % Dark brown
\definecolor{arsenic}{HTML}{3B444B}
\definecolor{darkGreen}{HTML}{00b300} % Dark green
\definecolor{tab:blue}{HTML}{1f77b4} % python
\RequirePackage{sectsty}
\chapternumberfont{\normalsize} 
\chaptertitlefont{\normalsize}
\RequirePackage[nostruts,compact]{titlesec}
\titlespacing{\chapter}{0in}{\UOneInChapterSpace}{\UHeadSpace}[0in] 
\titlespacing{\section}{0in}{0in}{\UDoubleSpace}[0in]
\titlespacing{\subsection}{0in}{0in}{\UDoubleSpace}[0in]
\titlespacing{\subsubsection}{0in}{0in}{\UDoubleSpace}[0in]
\titlespacing{\paragraph}{1em}{1ex}{1ex}[1em]
\titleformat{\chapter}
    [display]
    {\color{URED}\centering\normalfont\Large\bfseries\doublespacing}
    {\MakeUppercase{\chaptertitlename} \Large\thechapter}
    {0in}
    {\MakeUppercase}
    []
\titleformat{\section}
    [hang]
    {\centering\singlespacing\normalfont\Large\bfseries}
    {\thesection}
    {1ex}
    {}
    []
\titleformat{\subsection}
    [hang]
    {\centering\singlespacing\normalfont\large\bfseries}
    {\thesubsection}
    {1ex}
    {}
    []
\titleformat{\subsubsection}
    [hang]
    {\centering\singlespacing\normalfont\normalsize\bfseries}
    {\thesubsubsection}
    {1ex}
    {}
    []
\titleformat{\paragraph}
    [runin]
    {\centering\singlespacing\normalfont\normalsize\bfseries}
    {\theparagraph}
    {1ex}
    {}
    []
\titleformat{\subparagraph}
    [runin]
    {\centering\singlespacing\normalfont\normalsize\bfseries}
    {\thesubparagraph}
    {1ex}
    {}
    []
\parskip=0pt
\RequirePackage[final]{microtype}
\RequirePackage[defernums=true,
                hyperref,
                backref,
                backend=biber,
                style=ieee,
                natbib=true,
                refsegment=chapter,
                block=space
                ]{biblatex}
\setlength\bibitemsep{1.5\itemsep}
\defbibheading{references}[References]{% 
    \section{#1}
    \markboth{#1}{#1}%
    \singlespacing
}
\def\finalBibliography{
    {\singlespacing
    \printbibliography[heading=bibintoc, title={\uppercase{Bibliography}}] % Whole
    }
}
\RequirePackage{hyperref}
\hypersetup{pdfpagemode={UseOutlines},
    bookmarksopen=true,
    bookmarksopenlevel=0,
    hypertexnames=true,
    colorlinks=true,
    citecolor=darkBrown,
    linktoc=all,
    linkcolor=URED,
    urlcolor=midnightBlue,
    pdfstartview={FitV},
    unicode,
    breaklinks=true,
}
\RequirePackage{doi}
\RequirePackage{url}
\RequirePackage[capitalise]{cleveref}
\crefname{paragraph}{Paragraph}{Paragraphs}
\crefname{subparagraph}{Sub Paragraph}{Sub Paragraphs}
\captionsetup[sub]{labelsep=none, subrefformat=parens}
\RequirePackage[titles]{tocloft}
\renewcommand{\cftchapdotsep}{\cftdotsep}
\renewcommand{\contentsname}{\color{URED}\hfill \Large CONTENTS \hfill}
\renewcommand{\listfigurename}{\color{URED}\hfill \Large LIST OF FIGURES \hfill}
\renewcommand{\listtablename}{\color{URED}\hfill \Large LIST OF TABLES \hfill}
\setlength{\cftsecindent}{1em}
\setlength{\cftsubsecindent}{2em}
\setlength{\cftsubsubsecindent}{3em}
\setlength{\cftparaindent}{4em}
\setlength{\cftsubparaindent}{5em}
\RequirePackage{xfp}
\RequirePackage{xparse}
\renewcommand\cftchapdotsep{2}
\renewcommand\cftsecdotsep{2}
\renewcommand\cftsubsecdotsep{2}
\renewcommand\cftsubsubsecdotsep{2}
\renewcommand\cftparadotsep{2}
\renewcommand\cftsubparadotsep{2}
\renewcommand\cftchapafterpnum{\vskip2pt}
\renewcommand\cftsecafterpnum{\vskip2pt}
\renewcommand\cftsubsecafterpnum{\vskip2pt}
\setlength{\cfttabindent}{0em}
\setlength{\cftfigindent}{0em}
\RequirePackage{algpseudocode}
\RequirePackage{algorithm}
\def\thesistype#1{\gdef@thesistype{#1}}
\def\degreeAchieved#1{\gdef@degreeAchieved{#1}}
\def\department#1{\gdef@department{#1}}
\def\departmentLink#1{\gdef@departmentLink{#1}}
\def\submitdate#1{\gdef@submitdate{#1}}
\newcommand\skiplines[1]{\vspace{#1\baselineskip}}
\newcommand\thesisTitle{
    {
    \thispagestyle{empty}
    \begin{minipage}[c]{\textwidth}
        \vspace{1in}
        \centering
        \begin{spacing}{2}
            {\doublespacing\Large\bfseries\MakeUppercase{@title}}\
        \end{spacing}
        \large
        \skiplines{4}
        \begin{spacing}{2}
            by \
            @author \
        \end{spacing}
        \skiplines{4}
        A @thesistype ~submitted to the faculty of\
        University\
        in partial fulfillment of the requirements for the degree of \
        \skiplines{4}
        {@degreeAchieved}\
        \skiplines{4}
        \begin{spacing}{2}
            \href{@departmentLink}{@department}\
            \href{http://google.com}{University}\
            @submitdate
        \end{spacing}
    \end{minipage}
    \clearpage
    }
}
\def\copyrightyear#1{\gdef@copyrightyear{#1}}
\newcommand\copyrightpage{
    {\newpage
    \thispagestyle{empty}
    \topskip0pt
    \vspace{\fill}
    \noindent
    \begin{minipage}[c]{\textwidth}%
        \centering
        Copyright \copyright\ @author\ @copyrightyear \
        \skiplines{1} % university requirement
        All Rights Reserved
    \end{minipage}%
    \vspace{\fill}
    \newpage
    }
}
\def\committeeChair#1{\gdef@committeeChair{#1}}
\def\advisorTitle#1{\gdef@\advisorTitle{#1}}
\def\committeeMemberII#1{\gdef@committeeMemberII{#1}}
\def\committeeMemberIII#1{\gdef@committeeMemberIII{#1}}
\def\committeeMemberIIII#1{\gdef@committeeMemberIIII{#1}}
\def\committeeMemberIIIII#1{\gdef@committeeMemberIIIII{#1}}
\def\graduateDean#1{\gdef@graduateDean{#1}}
\def\departmentChair#1{\gdef@departmentChair{#1}}
\def\departmentChairTitle#1{\gdef@departmentChairTitle{#1}}
\def\deptmentCollegeSchool#1{\gdef@deptmentCollegeSchool{#1}}
\def\approvaldepartment#1{\gdef@approvaldepartment{#1}}
\def\chairDateApproved#1{\gdef@chairDateApproved{#1}}
\def\committeeMemberIIDateApproved#1{\gdef@committeeMemberIIDateApproved{#1}}
\def\committeeMemberIIIDateApproved#1{\gdef@committeeMemberIIIDateApproved{#1}}
\def\committeeMemberIIIIDateApproved#1{\gdef@committeeMemberIIIIDateApproved{#1}}
\def\committeeMemberIIIIIDateApproved#1{\gdef@committeeMemberIIIIIDateApproved{#1}}
\def\bfunderline#1{\underline{\kern 1in \textbf{#1}\kern 1in}}
\RequirePackage{tabularx} % pagewidth tables
\RequirePackage{array} % Specify width of tables
\RequirePackage{ragged2e} % Allows for justification of sections
\long \def \dissertationapproval{%
    \newpage
    \thispagestyle{empty}
    \vspace*{\fill}
    \noindent
    \begin{minipage}[c]{\textwidth}
        \centering
        \textbf{\Large University Graduate School} \
        \skiplines{2}
        \textbf{\Large STATEMENT OF DISSERTATION APPROVAL}
        \skiplines{2}
        %
        \justify
        \begin{doublespace}
            The dissertation of\hspace{1in}\bfunderline{@author} \
            \skiplines{2}
            has been approved by the following supervisory committee members:
        \begin{table}[H] % [htbp]
            \centering    \begin{tabular}{>{\centering\arraybackslash}p{0.6\textwidth}p{0.1\textwidth}>{\centering\arraybackslash}p{0.2\textwidth}}
                \bfseries{\@committeeChair} & \multicolumn{1}{l}{ , Chair} & \multicolumn{1}{c}{\bfseries{\@chairDateApproved}} \\
                \cmidrule{1-1}\cmidrule{3-3}          &       & \tiny{Date Approved} \\
                    &    &    \\ % add extra row between the committee members
                \bfseries{\@committeeMemberII} & \multicolumn{1}{l}{ , Member} & \multicolumn{1}{c}{\bfseries{\@committeeMemberIIDateApproved}} \\
                \cmidrule{1-1}\cmidrule{3-3}          &       & \tiny{Date Approved} \\
                    &    &    \\ % add extra row between the committee members
                \bfseries{\@committeeMemberIII} & \multicolumn{1}{l}{ , Member} & \multicolumn{1}{c}{\bfseries{\@committeeMemberIIIDateApproved}} \\
                \cmidrule{1-1}\cmidrule{3-3}          &       & \tiny{Date Approved} \\
                    &    &    \\ % add extra row between the committee members
                \bfseries{\@committeeMemberIIII} & \multicolumn{1}{l}{ , Member} & \multicolumn{1}{c}{\bfseries{\@committeeMemberIIIIDateApproved}} \\
                \cmidrule{1-1}\cmidrule{3-3}          &       & \tiny{Date Approved} \\
                    &    &    \\ % add extra row between the committee members
                \bfseries{\@committeeMemberIIIII} & \multicolumn{1}{l}{ , Member} & \multicolumn{1}{c}{\bfseries{\@committeeMemberIIIIIDateApproved}} \\
                \cmidrule{1-1}\cmidrule{3-3}          &       & \tiny{Date Approved} \\
            \end{tabular}%
        \end{table}%

        \justify
        and by \hspace{1in}\bfunderline{\@departmentChair}, {\@departmentChairTitle} of \\
        the {\@deptmentCollegeSchool} of \hspace{1in}\bfunderline{\@approvaldepartment} \\
        and by \bfunderline{\@graduateDean}, Dean of The Graduate School.\\
    \end{doublespace}
\end{minipage}
\vspace*{\fill}

}
\def\abstractString#1{\gdef@abstractString{#1}}
\newcommand\abstractPage{
    {\newpage
    \chapter*{Abstract}
        % manually set to page iii (University requirement)
        \setcounter{page}{3}
        \addcontentsline{toc}{chapter}{\uppercase{Abstract}}
        \hspace{\parindent}
        \begin{doublespace}
            @abstractString
        \end{doublespace}
    }
}
\def\dedication#1{\gdef@dedication{#1}}
\newcommand\dedicationPage{
    {\newpage
        \clearpage\thispagestyle{empty}\addtocounter{page}{-1} 
        \topskip0pt
        \vspace{\fill}
        \noindent
        \begin{minipage}[c]{.95\textwidth}%
            \centering
            @dedication
        \end{minipage}%
        \vspace{\fill}
    }
}
\def\frontispiece#1{\gdef@frontispiece{#1}}
\newcommand\frontispiecePage{
    {\newpage

        \clearpage\thispagestyle{empty}
        \topskip0pt
        \vspace{\fill}
        \noindent
        \begin{minipage}[c]{\textwidth}%
            \centering
            \includegraphics[width=\textwidth]{{@frontispiece}}
        \end{minipage}%
        \vspace{\fill}
    }
}
\RequirePackage{epigraph}
\def\epigraphQuote#1{\gdef@epigraphQuote{#1}}
\def\epigraphAuthor#1{\gdef@epigraphAuthor{#1}}
\newcommand\epigraphPage{
    {\newpage
        \clearpage\thispagestyle{empty}
        \topskip0pt
        \vspace{\fill}
        \noindent
        \begin{minipage}[c]{\textwidth}%
            \centering
            \epigraph{\Large{@epigraphQuote}}{---{@epigraphAuthor}}
        \end{minipage}%
        \vspace{\fill}
    }
}
\def\Acknowledgement#1{\gdef@Acknowledgement{#1}}
\newcommand\AcknowledgementPage{
    {
    \chapter*{Acknowledge}
    \addcontentsline{toc}{chapter}{\uppercase{Acknowledge}}
    \hspace{\parindent}
    \begin{doublespace}
        @Acknowledgement
    \end{doublespace}
    }
}
\def\NotationAndSymbols#1{\gdef@NotationAndSymbols{#1}}
\newcommand\NotationSymbolsPage{
    {
    \chapter*{Notation and Symbols}
        \addcontentsline{toc}{chapter}{\uppercase{Notation and Symbols}}
        \begin{center}
            @NotationAndSymbols
        \end{center}
    }
}
\RequirePackage{fancyhdr}
\newcommand\frontMatter{%
    \cleardoublepage
    \pagenumbering{roman}}
\newcommand\mainMatter{%
    \addtocontents{toc}{\vspace{1em}\noindent{\bf\uppercase{Chapters}}\hfill\par} 
    \cleardoublepage
\pagestyle{fancy}
\fancyhf{} 
\lhead{} 
\rhead{\thepage} 
\renewcommand{\headrulewidth}{0pt} 

\fancypagestyle{plain}{%
  \renewcommand{\headrulewidth}{0pt}%
  \fancyhf{} 
  %\fancyhead[R]{\thepage} 
}

\pagenumbering{arabic} 
\doublespacing 

}
\newcommand\backMatter{%
    \if@openright
    \cleardoublepage
    \else
    \clearpage
    \fi
    % @mainmatterfalse
}
\renewcommand\cftfigafterpnum{\vskip5pt\par}
\renewcommand\cfttabafterpnum{\vskip5pt\par}
\newcommand\tableOfContents{
    {
    \hypersetup{linkcolor=blue}
    \clearpage
    \pdfbookmark{Table of Contents}{toc}
    \tableofcontents
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{\uppercase{List of Figures}}
\listoffigures

\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{\uppercase{List of Tables}}
\listoftables
}

}
\pdfstringdefDisableCommands{\let\uppercase\relax}
\RequirePackage{mwe}
\endinput

Here is my StudentInfo.tex file:

\author        {Full Name}
\title        {Thesis title}
\thesistype    {dissertation}
\degreeAchieved    {Doctor of Philosophy}
\department    {Department of xx}
\departmentLink    {}
\submitdate    {xx yyyy}
\copyrightyear  {\the\year{}}
\abstractString    {Abstract goes here.  \\indent More info here.}
\dedication    {To Science!}
\frontispiece    {example-image-a} %
\epigraphQuote    {``Quote"} 
\epigraphAuthor    {Famous Individual}
\Acknowledgement{Acknowledge \ldots \\indent more recognition.}
\NotationAndSymbols{
\begin{tabular}{p{0.05\textwidth}p{0.9\textwidth}}
    \toprule
    x     & \emph{Var} - the variable x. \
    \bottomrule
\end{tabular}%
}
\approvaldepartment     {Dept.}
\graduateDean           {xx}
\departmentChair        {yy}
\departmentChairTitle   {Chair}
\deptmentCollegeSchool  {Department}
\committeeChair         {Advisor}
\advisorTitle           {Associate Professor, Associate Chair}
\committeeMemberII      {xx}
\committeeMemberIII     {yy}
\committeeMemberIIII    {zz}
\committeeMemberIIIII   {aa}
\chairDateApproved                  {xx xx \the\year{}}
\committeeMemberIIDateApproved      {xx xx \the\year{}}
\committeeMemberIIIDateApproved     {xx xx \the\year{}}
\committeeMemberIIIIDateApproved    {xx xx \the\year{}}
\committeeMemberIIIIIDateApproved   {xx xx \the\year{}}

Here is my bibliography.bib file

@article{test,
author = {Last, First},
doi = {xxxx},
issn = {xxx},
journal = {ABC},
number = {1-2},
pages = {12--22},
title = {{Title}},
volume = {111},
year = {xxxx}
}

Last but not least, here is the MWE that calls the cls and student info file

% The class file specifying the document structure
\documentclass{MastersDoctoralThesis}
\input{StudentInfo.tex}
\addbibresource{bibliography.bib}
\begin{document}
    \frontMatter
    \begin{center}
        \thesisTitle
        \copyrightpage
        \dissertationapproval
    \end{center}
    \abstractPage
    \dedicationPage
    \frontispiecePage
    \epigraphPage
    \tableOfContents
    \NotationSymbolsPage
    \AcknowledgementPage
\mainMatter
\chapter{\uppercase{Introduction}}\label{Chapter1}
    \section{Overview}
        \lipsum[1] \cite{test}

    \section{Background and significance}
        \lipsum[1-3]

    \section{Hypothesis and Rationale}\label{Hyptohesis_Rationale}
    \subsection{Aim 1}\label{aim:1}
        \lipsum[1]

    \subsection{Aim 2}\label{aim:2}
        \lipsum[2]

    \subsection{Aim 3}\label{aim:3}
        \lipsum[3]

    \section{Impact and Intellectual Contributions}\label{sec:impact}
        \lipsum[1-2]

    % Bibliography
    \printbibliography[segment=\therefsegment, heading=references]

\chapter[\uppercase{Multiline title}]{\uppercase{Multiline \protect\\ title}}\label{Chapter2}

    \lipsum[1]

    \section{Abstract}
        \lipsum[1]

    \section{Introduction}
        \lipsum[1-5]

    \section{Section1}\label{sec:Section1}

    \subsection{Subsection1}\label{subsec:Subsection1}
        \lipsum[1-2]

        \begin{figure}[tbp]
            \centering
            \begin{subfigure}[b]{0.3\textwidth}
                \centering
                \includegraphics[width=\linewidth]
                {example-image-a}
                \subcaption{\label{fig:a}}
            \end{subfigure}%
            \begin{subfigure}[b]{0.3\textwidth}
                \centering
                \includegraphics[width=\linewidth]
                {example-image-b}
                \subcaption{\label{fig:b}}
            \end{subfigure}%
            \begin{subfigure}[b]{0.3\textwidth}
                \centering
                \includegraphics[width=\linewidth]
                {example-image-c}
                \subcaption{\label{fig:c}}
            \end{subfigure}%
            \caption{\subref{fig:a} \ldots \subref{fig:b} \ldots \subref{fig:c}
            \ldots}
            \label{fig:Figure_1}
        \end{figure}

        \lipsum[1-2]

    \subsection{Subsection2}\label{subsec:Subsection2}
        \lipsum[1-2]

        \begin{figure}[tbp]
            \centering
            \begin{subfigure}[b]{0.9\textwidth}
                \centering
                \includegraphics[width=\linewidth]
                {example-image-a}
                \subcaption{\label{fig:d}}
            \end{subfigure} \\[1ex]
            \begin{subfigure}[b]{0.45\textwidth}
                \centering
                \includegraphics[height=5cm]
                {example-image-b}
                \subcaption{\label{fig:e}}
            \end{subfigure}%
            \begin{subfigure}[b]{0.45\textwidth}
                \centering
                \includegraphics[height=5cm]
                {example-image-c}
                \subcaption{\label{fig:f}}
            \end{subfigure}
            \caption{\ldots \subref{fig:d} \ldots \subref{fig:e} \ldots
            \subref{fig:f} \ldots}
            \label{fig:Figure_2}
        \end{figure}

    \subsection{SubSection3}\label{subsec:Subsection3}
        \lipsum[1-2]

    \paragraph{Paragraph1}\label{par:Paragraph1}
        \lipsum[6-7]

        \begin{figure}[tbp]
            \centering
            \begin{subfigure}[b]{0.5\textwidth}
                \centering
                \includegraphics[width=\linewidth]
                {example-image-a}
                \subcaption{\label{fig:g}}
            \end{subfigure}%
            \begin{subfigure}[b]{0.5\textwidth}
                \centering
                \includegraphics[width=\linewidth]
                {example-image-b}
                \subcaption{\label{fig:h}}
            \end{subfigure}%
            \caption{\ldots \subref{fig:g} \ldots
            \subref{fig:h} \ldots} 
            \label{fig:Figure_3}
        \end{figure}

    \paragraph{Paragraph2}\label{par:Paragraph2}
        \lipsum[8-10]

        \begin{figure}[tbp]
            \centering
            \includegraphics[width=0.5\textwidth]
            {example-image-a}
            \caption{\ldots} 
            \label{fig:Figure_4}
        \end{figure}

        \lipsum[66]

        \begin{figure}[tbp]
            \centering
            \includegraphics[width=0.5\textwidth]
            {example-image-16x10}
            \caption{\ldots} 
            \label{fig:Figure_5}
        \end{figure}

        \lipsum[75]

    \subsection{SubSection4}\label{subsec:Subsection4}
        \lipsum[10-12]
\appendix
\finalBibliography

\end{document}

On page #11 I was able to recreate the spacing issue. I'm just not sure how to make the spacing between sections/subsections/paragraphs/subparagraphs all the same. I did make spacing above and below figures/tables/algorithms the same.

Thank you!

Answer 1

UPDATED

I used a simplified MWE from the one posted to illustrate the problem.

The additional space you are viewing is, in a sense, an artifact of this particular page because of the float.

The class sets all title spaces. Also inserts before and after the figure environment (also table and equation) a 3ex space using \addvspace. When a float is pushed to the top of the page, this space is not added.

3ex is slightly larger than a baselineskip and this extra space is inserted before Paragraph2, who shows four lines in the page.

A solution is to change in MastersDoctoralThesis.sty \AtBeginEnvironment{figure}{\addvspace{\UHeadSpace}} to \AtBeginEnvironment{figure}{}

Wrong spacing before \paragraph

Using \AtBeginEnvironment{figure}{} in MastersDoctoralThesis.sty.

Now Paragraph2 shows five lines in the page.

% !TeX TS-program = pdflatex
\documentclass{MastersDoctoralThesis}
\usepackage{showframe} % show the margin
\begin{document}
\section{Section1}

\subsection{Subsection1}
\lipsum[1-2]
\subsection{Subsection2}
\lipsum[1-2]
\subsection{SubSection3}\label{subsec:Subsection3}
\lipsum[1]
\paragraph{Paragraph1}

\lipsum[1-2]

\setlength{\UHeadSpace}{0pt}  % add before \begin{figure} <<<<<<<<<
\begin{figure}[tbp]
    \centering
    \begin{subfigure}[b]{0.5\textwidth}
        \centering
        \includegraphics[width=\linewidth]
        {example-image-a}
        \subcaption{\label{fig:g}}
    \end{subfigure}%
    \begin{subfigure}[b]{0.5\textwidth}
        \centering
        \includegraphics[width=\linewidth]
        {example-image-b}
        \subcaption{\label{fig:h}}
    \end{subfigure}%
    \caption{\ldots \subref{fig:g} \ldots
    \subref{fig:h} \ldots} 
    \label{fig:Figure_3}
    \setlength{\UHeadSpace}{3ex} % add before \end{figure}  <<<<<<<<<<
\end{figure}
\paragraph{Paragraph2}

\lipsum[1]

2   \lipsum[2]
\end{document}

Going back to the posted MWE, using \AtBeginEnvironment{figure}{} the page #11 appears now with seven lines under Paragraphs2 and no space anomalies.