Re: Good PDF converter or reader?
If the PDFs are authored by professionals who know a thing or two about math/physics, they're probably doing so by writing it in LaTeX. Your best bet is to get the LaTeX source and using something like Pandoc to convert it into a more readable format you can work with. Having some context regarding the content you're trying to read would also help.
To @3's point about reading mathematical notation, I also went the human reader/tutor route. It was highly effective for me. I'm most certainly not trying to discourage you from finding solutions to read the material on your own, but it is exceedingly difficult, and I don't know that anyone is working on ways to help solve the problem.
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