Hi mdmuddin,
your can "force" your Cover Story to use the font you want. It's quite hard work if you do it for first time.
You have to edit the epub either by calibre or sigil (or something similar), to be exact, you must edit stylesheet.css file. (and use fonts embedded to the book or loaded to "font" folder of your Cover Story)
try
this thread, you can find answers there.
I hope this will help.
