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As far as PDF performance with highlighting and note-taking - no one knows. These are new features for PDF on Kindle 3, which hasn't yet begun to ship. I can tell you that adding 60 bookmarks to a single PDF doesn't create a noticeable delay. I use a lot of bookmarks because Kindle doesn't support PDF links, including those in the table of contents. Another thing to consider is PDF reflow. If you're accustomed to resizing PDF text on your 900, you will miss that functionality on the Kindle 3.
It is rumored that Kindle DX Graphite will soon incorporate the same PDF functionality as the new Kindle 3. If this comes about, then DX would make a much better choice for PDF reading, since the screen size allows you to easily read PDFs without needing to enlarge the text.
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