After several more tries, I finally processed the hardest of these files... so none are completely broken.
I don't know if it caused any of the trouble, but I uninstalled Malwarebytes for the time being.
Here is a free pdf which gave me a lot of trouble though:
https://gallica.bnf.fr/ark:/12148/bpt6k6348270v (there's an option to download the book as a pdf.)
When running in the command line with -mode copy -dev dx, I was getting frequent seg faults. I still get some.
When running in the Mac Automator, I get other error messages, and the Automator still often drops out when the regular interface would keep going.