A good way to get help with this sort of thing is to pose an example questions as a reprex (or as close to a reproducible example as possible). FAQ: Tips for writing R-related questions.
It's not totally clear to me the problem that you're having, but there are a number of R packages that may help. These are all in the aim of getting your pdf and xml data into something you can work with in R.
pdftools, for extracting text, fonts, attachments and metadata from a PDF file
xml2 is a handy tidyverse package for working with HTML and XML from R