Quick update: since the system got deployed I did a lot of testing (and a lot of no-sleep, you'll see why) and figured out many bugs. Really shows how important testing is since not catching those errors would've meant hours of reviewer time lost!
In a nutshell, I had to re-engineer many parts of the system for the automated building and merging of PDFs. Instructions will be added shortly on the Github.
We expect the system to be used in production on short notice.