So I'm just popping in here to confirm that I am in fact not dead, just kind of crushed by my current practicum. It's terribly organized and far more work than anyone had expected, which is why I basically lost most of my free time. I'm halfway through this abomination however, so while I won't really be doing much of anything for the next two weeks, you can except me to return after that.
Also, how did you determine what the max possible length for a PAPA file is? Is there any explicit threshold that you figured out or did you just add all the overworld messages to one file and the event dialogue to another?
Regarding the editing of the script files - I dunno, but I feel that it should be your choice really? While I would obviously be very grateful for your help, I don't really want to pile more work onto you if you're busy anyways, so...
Regardless of that: I checked out the cmn.rar you had attached to your post and am not sure why you included two different Npc.nut files? If I compare it to my own romfs, I find one of them in the Script/Util folder, but none directly in the Script folder itself.