Maybe this is old news, but I found that the height of PDF pages is of critical importance. When reading sideways, the reader goes to great lengths to ensure that the zoom makes a page into two screenfulls (with a 2-line overlap). By trimming off the headers and footers on your PDFs (easily done in acrobat - you can do all pages in one shot), the reader zooms in much tighter. The downside is that you've trimmed off the page numbers, but I think that's a small price to pay.
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