The easiest way to handle this would most likely be to use the command line tools and scripting.
Don't use calibre libraries. Instead use a folder with all the books that you prepare using calibre and save to disk. And perhaps another folder with the fonts.
For each font and book combination, convert and save the converted book to a new folder named after the font. Two loops. One loop over the fonts, the other over the books, inside the other.
See:
http://manual.calibre-ebook.com/cli/ebook-convert.html
Test it with three fonts and three books until you get it working.
If you want to you can import the books to separate calibre libraries afterwards. Or change the metadata for the books to include the font name in the title, and import all to the same calibre library and use virtual libraries instead.
If you don't have the necessary programming/scripting skills, then hire someone that has. It is not very advanced.