I've been wrestling with a similar set of tasks, and have arrived at a similar set of tools and options.
How you process PDF depends greatly on the scale at which you're working with documents. For large-volume, high-speed processing, automation is necessary. Where you're translating a more stable corpus, human input may be tractable. The ability to look at source PDF, OCR, and an edited text version to correct for errors seems a part of that workflow.
Often it's possible to get close or approximate transcription using standard tools. I've found the Poppler library's "pdftotext" remarkably good with many PDFs, so long as there's some text within them: https://poppler.freedesktop.org
There's a general concept I've been working toward of a minimum sufficient document complexity, which follows a rough (though not strict) hierarchy. It's remarkable how much online content is little more than paragraph-separated text, with no further structure. Even images are not strictly informational, but rather window-dressing.
Typically, additional elements added are hyperlinks, images, text emphasis (italic and bold, often only the first), sections, lists, blockquotes, super- and sub-script, in roughly that order.
(A study looking at the prevalence of specific semantic HTML elements within a corpus would be ... interesting.)
Then there are the elements NOT natively supported in HTML: equations, endnotes/footnotes, tables of contents, etc.
It seems to me there should be an analogue to Komolgrov complexity as concerns layout of textual documents. That is: there is a minimum necessary and sufficient level of markup (perhaps: number, type, and relationship of elements) necessary to lay out a specific work.
I've tagged out novel-length books in Markdown with little more than the occasional italic and chapter marks.
Documents which use more markup than is required are overspecified. This is the underlying problem with a great deal of layout, and the ability to reduce texts to their minimum complexity would be useful. It's a nontrivial problem, though large swathes of it should be reasonably achievable.
Another approach would be for information-exchange formats to actually be, you know, information exchange formats rather than PDF.
(Though the latter is often, though not always, well-suited to reading.)