Calibre manual actually states that PDF is the worst input format for conversion. The formatting issue you are experiencing with increased font size is actually a "feature" - reflow. If you open a PDF file in Adobe Reader and turn reflow on, you'll get the same effect.
I don't have much experience in fiddling with PDF other than cropping white margins with Adobe Acrobat. This seemed to help things on my Irex Iliad.
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