If you find you need more flexible search/replace and other text processing functionality and you want to use the same rules on a whole batch of files at once, you might want to look at
http://www.datamystic.com/textpipe.html. It's not free, but the "lite" version is under US$50. I'm using the "pro" version for another (non ebook related) task and it's quite powerful, and fairly easy to use. (I have no other connection with this company or product.)