I had a problem converting embedded images and fonts from Markdown to EPUB; this script helps by piggy-backing on the epub-embed-font option to include images:

    #!/bin/bash

    FILENAME=$(cat title.txt).epub
    CSS=style.css
    IMAGES_DIR=images

    # Ensure images get embedded into the document.
    for url in $(grep image $CSS | grep url | sed 's/.*url( *\(.*\) *).*/\1/g'); do
      EMBED="$EMBED --epub-embed-font=$IMAGES_DIR/$url"
    done

    # Generate the ePub, including fonts and images.
    pandoc \
      --smart \
      --epub-cover-image=cover/cover.png \
      --epub-metadata=metadata.xml \
      --epub-stylesheet=$CSS \
      --epub-embed-font=fonts/MyUnderwood.ttf \
      $EMBED \
      -t epub -o $FILENAME output/*.vars

The .vars files are chapters that have their variable names substituted for values, such as:

    for i in chapter/*.md; do
      out=$OUTDIR/$(basename $i);
      cat variables.yaml $i > $out;
      pandoc $out --template $out > $out.vars

      cat $out.vars | sed -e 's/;;/\$/g' |\
        pandoc --chapters -t context -o $OUTDIR/$(basename $i .md).tex;
    done

A handy trick to avoid duplication (of names, places, or any text really) within the content.