I believe that default.pl is only brought into play when there is no quest file for an NPC. If there is a quest file in place, the server will use it.
So what you'd wind up doing is wiping all the normal PEQ quest files, modifying your default.pl file, and then going through each zone's folder and deciding which quest files you can bring back in entirely (for NPCs that wouldn't be killed [quest-givers, merchants, GMs of each class, etc.) and then figuring out which ones are for NPCs that will be killed and to modify their scripts accordingly.
It's going to be very painful and tedious if you do it that way, but it would make it possible with the existing tools available to you.
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