I think you could just add options with checkboxes like there are now...
-Search and Replace This Line Only
-Search and Replace The Next [variable] Lines. (where [variable] is a text box that only numbers can be entered into)
-Search and Replace Text on a new line only (Specified by <br> or <p>)
-Search and Replace All Documents with [variable] in the filename (where [variable] is a text field where any characters can be entered into)
Oh, yes, and of course, be able to search and replace multiple lines.