If the original poster is still looking for a solution, I attach my private little hack of modify_epub. It is a totally stripped down thing, just searches for some regexes, removes fonts and smartens punctuation.
To individualize it, extract main.py and open it in a simple texteditor (notepad++ for example).
Only thing that needs to be changed is in MY_REGEXES. What to do should be self-explinatory. No need to understand python, just copy/paste the lines and change the regex string.
Now put the new main.py back in the archive and import it in calibre via "load plugin from file". There is now a button in the toolbar to do the search and replace stuff.
Of course this is not rigidly tested and without any guaranties
