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This is a late reply and you've probably solved the problem, but for the record...
The Notepad++ macro files are not very helpful unless you know what the command numbers mean, and I haven't seen documentation for this. The problem is that when you record a macro that opens a dialog box and then puts the input focus back on the text, all those actions are recorded. If you can figure out which commands are opening or switching focus to the search window, you can just delete them and do all the editing "silently."
My solution to the problem was to turn to Visual Studio, where macro files are much more easily understood and edited.
As far as curly quotes go, though, you're reinventing the wheel. Calibre will do this for you, and if you don't use Calibre, you can run the same Python script they use; google "SmartyPants".
cheers,
Peter
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