Unfortunately, I have to recall all this from memory as the system I'm working on now does not have epub searching configured.
What tickled my memory was your mentioning of iFilter: I remember that I did certainly installed some additional ones, at least a PDF iFilter. I do remember that I did some tweaking to get it to work.
That said: at that time when using a "search string", WS returned:
- epub files of which the file name comprised the "search string";
- epub files in which the epub contents contained the "search string".
Obviously, the latter situation was what I was after, but I cannot remember the details how I got there.