I've now got the PIF board fully emulated (unfortunately it's all I've got emulated) and I have been able to step through a bunch of the code that had me stumped before.
I just stumbled upon an Easter Egg in the code in the form of a guy's name: Rich Witt. I assume he worked for Williams and wrote this ROM program. Anyone know anything about him? I had a hard time figuring out it was a person's name because in order to decode it, I had to clear the high bit before doing an ASCII lookup. (The apple2 uses this 'non-standard' ASCII also which gave me the idea that it might be ASCII in the first place and try to parse it)
I've updated my wiki page with a bunch more info that I didn't have when I made my original post (and will continue to do so).