In some cases I suspect those same files are available at project Gutenburg or similar site (manybooks, etc) Many of those sites allow you to choose your format.
Personally I've never really liked the options for pdf files, as by the time its big enough to read, I have to scroll for each page. And that gets to be a big pain after 50 pages or so.
Again I can only speak for myself, but I have been quite happy converting pdf's with a free PDF converter. (Zilla) Or getting them from a site where I can control the format.
If you wanted to post one of your pdf's your having issues with I'd be glad to see if I can convert it.
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