Depending on the document I do one of the following:
1. If the document is mainly text, I copy the text to a text editor, do whatever I want with it and then convert it back to pdf. I did this with the last book I read because I didn't like the font.
2. If the document is "format"-heavy with pictures and tables, I extract jpgs from the pdfs. This means you'll have to "scroll" around one page, but at least you keep the formatting. And the reader handles pictures better in this case than if it is the pdf. I had to reset the reader several times when I tried to open more complex pdfs. You have to be careful with the resolution settings for the jpgs though. If it's not enough, you'll get nice small files that load fast, but they're almost unreadable, even when magnified.
I don't know if all image editing programs open up pdfs, but some do and they offer anti aliasing which provides smoother text when converted to jpg.
I'm not sure if this helps, but maybe it does.
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