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Incomplete iffalse error and “Tex capacity exceeded” [on hold]

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I’m getting these error messages when I try to compile (XeLaTeX) my dissertation on texpad for Mac OS/X running TexLive2015, this is what I get:

./Dissertation.tex:94: Incomplete iffalse; all text was ignored after line 290.
<inserted text> 
                fi 
l.94 begin{document}

./Dissertation.tex:94: TeX capacity exceeded, sorry [input stack size=5000].
blx@dopreamblecmds ->do blx@dopreamblecmds 
                                              do blx@onlypreamble 
l.94 begin{document}

No pages of output.

I never had this problem before. It used to work like a charm until I added one footnote. One of the issues is clearly related to my bibliography, and in fact, a few lines above I can read:

Package biblatex Warning: File 'Dissertation.bbl' is wrong format version - expected 2.5.

Package biblatex Warning: The following entry could not be found
(biblatex)                in the database:
(biblatex)                type X <return> to quit.
(biblatex)                Please verify the spelling and rerun
(biblatex)                LaTeX afterwards.

and at the end of the dissertation.bbl file I find this error:

 endentry
  endsortlist
  missing{type  X <return>  to quit.}GenericError {               }{LaTeX Error: Something's wrong--perhaps a missing item}{See the LaTeX manual or LaTeX Companion for explanation.}{Try typing  <return>  to proceed.MessageBreak If that doesn't work}
  missing{subsubsectionblock def subsubsection{subsubsection}par @tempskipa beforesubsubsecskip relax let GenericError {               }{LaTeX Error: Something's wrong--perhaps a missing item}{See the LaTeX manual or LaTeX Companion for explanation.}{Try typing  <return>  to proceed.MessageBreak If that doesn't work}
  missing{The marquis Federico Cavriani's views}
  missing{type  X <return>  to quit.}let reserved@d =*def par}
endrefsection
endinput

But it’s hard for me to understand why iffalse and “Tex capacity exceeded” errors appear at the same time. I use a template from my university in order to comply with the graduate school’s formatting rules. I tried to adapt this template for a dissertation in the humanities and I added the necessary packages.

documentclass[12pt,letterpaper,oneside,final]{memoir}
usepackage[no-math]{fontspec}
usepackage{xltxtra}
setmainfont[Mapping=tex-text,Ligatures={Common}]{Garamond Premier Pro}
usepackage{xkeyval}
usepackage{polyglossia}
usepackage{graphicx}
graphicspath{ {images/} }
usepackage[rightcaption]{sidecap}
usepackage{float}
usepackage{url}
usepackage{type1cm}
usepackage{lettrine}
setdefaultlanguage[variant=american]{english}
setotherlanguage[variant=ancient,numerals=arabic]{greek}
setotherlanguage[spelling=new]{german}
setotherlanguages{latin,french,italian,spanish}
usepackage{csquotes}
usepackage{etoolbox,keyval,ifthen}
usepackage{csquotes}
usepackage[backend=biber]{biblatex-chicago}
%DeclareAutoCiteCommand{plain}{cite}{cites}
DeclareAutoCiteCommand{plain}{textcite}{textcites}
DeclareAutoCiteCommand{inline}{textcite}{textcites}
DeclareAutoCiteCommand{footnote}[l]{footcite}{footcites}
%DeclareAutoCiteCommand{footnote}[f]{smartcite}{smartcites}
bibliography{masterbib}
usepackage[final]{hyperref}%?%hyperfootnotes=false
hypersetup{bookmarks=false,        % show bookmarks bar?
    unicode=true,           % non-Latin characters in Acrobat’s bookmarks
    pdftoolbar=true,        % show Acrobat’s toolbar?
    pdfmenubar=true,        % show Acrobat’s menu?
    pdffitwindow=false,     % window fit to page when opened
    pdfstartview={FitH},    % fits the width of the page to the window
    pdftitle={},
    pdfauthor={XXXXXXXXXXXXXXXXXX},     % author
    pdfsubject={Ph.D. Dissertation},   % subject of the document
    pdfcreator={XXXXXXXXXXXX},   % creator of the document
    pdfproducer={XXXXXXXXXXXXX}, % producer of the document
    pdfkeywords={XXXXXXXXXXXXX}, % list of keywords
    pdfnewwindow=true,      % links in new window
    colorlinks=true,       % false: boxed links; true: colored links
    linkcolor=black,          % color of internal links
    citecolor=black,        % color of links to bibliography
    filecolor=black,      % color of file links
    urlcolor=black           % color of external links
}
usepackage{microtype}
usepackage{xecolor}
definergbcolor{blue}{0000FF}
definergbcolor{red}{FF0000} %textxecolor{colorname}{text}
XeTeXdashbreakstate=1
usepackage{indentfirst}
usepackage{outline}
usepackage{verbatim}
usepackage{enumerate}
usepackage{longtable}
usepackage{ccicons}
usepackage{bookmark}
usepackage{etoolbox}
%!%%%%%%%%%%%%%%%%%%%%%for non-italicized headings%%%%%
% http://tex.stackexchange.com/questions/32655/remove-italic-from-memoir-headings-pagestyle
makeevenhead{headings}{leftmark}{}{}
makeoddhead{headings}{rightmark}{}{}
makeevenfoot{headings}{}{thepage}{}
makeoddfoot{headings}{}{thepage}{}

%!%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%!%%%%%%%%%%%%%%%%%%%%%for margins, l=1.5; rest=1.0, maybe add 0.1in%%%%%
setstocksize{11in}{8.5in}
settrimmedsize{11.0in}{8.5in}{*} %settrimmedsize{ height }{ width }{ ratio }
settypeblocksize{7.75in}{5.8in}{*} %settypeblocksize{ height }{ width }{ ratio } %note: 7.25h gives margins of 1.5 on top/bottom w/ ubratio of 1
setlrmargins{1.5in}{*}{*} %setlrmargins{ spine }{ edge }{ ratio } %spine = left, edge = right; only answer one or two of these values
%setlrmarginsandblock{1.5in}{1.0in}{*} %setlrmarginsandblock{ spine }{ edge }{ ratio } %
%setulmargins{*}{*}{*} %setulmargins{ upper }{ lower }{ ratio }
%setulmarginsandblock{0.5in}{*}{*} %setulmarginsandblock{ upper }{ lower }{ ratio }
%setheadfoot{*}{*} %setheadfoot{ headheight }{ footskip }
%setheaderspaces{1.0in}{*}{*} %setheaderspaces{ headdrop }{ headsep }{ ratio }
%checkandfixthelayout[lines]
flushbottom
%!%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
apptocmd{sloppy}{hbadness 10000relax}{}{}

setsecnumdepth{subparagraph}
makeatletter
renewcommand@makefntext{hspace*{2em}@thefnmark. }
newenvironment*{singlespcquote}
        {quoteSingleSpacing}
        {endquote}
SetBlockThreshold{0}
SetBlockEnvironment{singlespcquote}
SetCiteCommand{parencite} %default is cite

begin{document}
%fussy
%hyphenpenalty=5000   %1000 default=?
%tolerance=1000        %1000 %200= default
%setlength{emergencystretch}{3em}
%midsloppy
fussy
vbadness=10000 % badness above which bad vboxes are shown. (Default = 10000?)
frontmatter
hyphenation{}

DoubleSpacing

begin{center}

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