[jbuckh]

I wanted to write my solution here in case anyone else needs it.

I send my pdf which was created by Calibre through pdflatex to create page numbers. Below I copied my .tex file that is being sent to pdflatex. pdf.pdf is the name of the Calibre generated pdf.

\documentclass[8pt]{article}
\usepackage[final]{pdfpages}
\usepackage{fancyhdr}

\topmargin 70pt
\oddsidemargin 70pt

\pagestyle{fancy}
\rfoot{}
\cfoot{\Large\thepage}
\renewcommand {\headrulewidth}{0pt}
\renewcommand {\footrulewidth}{0pt}

\begin{document}
\includepdfset{page=1,pagecommand=\thispagestyle{e mpty}}
\includepdf{pdf.pdf}
\includepdfset{pages=2-,pagecommand=\thispagestyle{fancy}}
\includepdf{pdf.pdf}
\end{document}

This tex file will place a page number on the center of each page. It will also ignore the first page (mine is a cover image that does not need a page number).

The command I used is here:

pdflatex -output-directory=directory {tex file name}