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I would assume it would be somewhat dependent on how the books was originally laid out. Still, if the 3rd level is "too big" (for aesthetic purposes, I presume?) it seems you may want to try converting the PDF to a different format. As you've probably read, PDFs are the trickiest format to convert in that they are designed to be "fixed" in terms of layout. They don't "re-flow" naturally, the way most web pages can when you change the font-size or make the window smaller.
You can use Calibre to convert PDFs to another format, but unless you're good at crafting "regular expressions" ("regex") to eliminate page numbers, headers, footers and such, you are probably going to find them appearing in the midst of your text, which could prove annoying. I've had some success converting PDFs to HTML with MobiPocket Creator, using "regex" in a text editor to remove the unwanted code. (For some reason, I can't apply my limited regex knowledge to Calibre itself, otherwise I'd try to do it all there.)
Once you've got your book in HTML, you can apply CSS (styles) to get the font size(s) that are most comfortable for you. Calibre gives you a way to do this, I believe. From HTML you can easily convert to the other formats Calibre supports.
If I were you and in a hurry, I'd try running the PDF through Calibre and see if I liked the results. If the header/footer/page number stuff was sufficiently distracting, I might want to pursue techniques for removing it. Otherwise, just try to ignore it.
Good Luck!
(And I suspect you'll get some even better responses as time goes on as you're probably not alone with this issue.)
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