First, unless it changed in the 2.5 update, you cannot highlight in a PDF file.
For regular Kindle files, the main storage for highlights, bookmarks, and notes, is in the .mbp file that matches the .azw file. An extra copy is placed in the "My Clippings.txt" file, which you can copy to your pc, and use as you wish.
If you need to highlight things in a pdf, if the format is not too fancy, you can convert it to a Kindle file (.mobi). Then, you can highlight things.
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