There are no settings that apply to all books. If you are having a particular problem with a particular book and you want help, then you need to post a sample that demonstrates the problem on conversion. In general, if your epub file was made by someone incompetent and contain lots of font size settings in different types of units (device dependent vs. device independent), you are never going to get a conversion that is 100% accurate, you will see the same problems doing an epub to epub conversion as well.
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