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What works for me is ePub and IBooks as well.
I have also found that if I reconverted from ePub to ePub, told it to maintain cover aspect ratio cos that looks better and insert meta data as first page it gives me results I like.
on the convert window, cover aspect ratio is on the ePub output tab and insert meta deta is on the structure detection tab.
The reason I don't choose PDF files is because ePub can reflow, so no scrolling issues if I increase the font.
Now, what would be very nice would be a calibre reader and or management program for the iPad. Alas, I don't own a Mac or know anything about the apple environment besides on this iPad that keeps auto correcting me.
Your mileage may vary!!
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