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Go into your calbre preferences -> pdf input to change the default back to 0.45, sounds like you've been doing it on a book by book basis in the individual book's conversion options. You may also need to uncheck the box that says to use the individual settings for the books since you've converted them before, not sure if 0 got saved at the book level.
The other junk looks like spam put in by a trial version of ABBYY. You'll need to write a header or footer removal regex to get rid of it.
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