I did a diff on the two readhmid outputs from the re-flashed one vs. another one that I hadn't touched and they were the same for the pins in question. So either the flash didn't take or something else is broken. (there were other differences in the two files)
In any event for now I'm going to go back to making a DB-25 converter since I've exceeded my rabbit hole depth limit
Thank you for sticking with me.