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The short answer is that there is currently no way to do what you want.
To do what you want requires software support for it. While the calibre viewer supports making bookmarks, there isn't a way to add them externally. And the viewer doesn't support the annotations part. I believe this is part of Kovid's plans, but I have no idea when.
Until then, the best I can suggest is to select some text on the page and save that as a highlight. Then use the Annotations plugin to fetch them into calibre. Then you can do a search using the selected text. I do this all the time while correcting errors in the book. I select enough text so that I can find it easily and can see what the error is. I only add an annotation if the correction is not obvious.
I should add that when the calibre viewer supports annotations fully, I will be updating the Annotations plugin to use it. I'm both looking forward to it, and dreading it.
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